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Thesis (Ph.D.)--Boston University / PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you. / We have constructed a database of hydroxyl radical (•OH) cleavage patterns of DNA in order to investigate the relationship between the sequence of a DNA molecule and its three-dimensional structure. The hydroxyl radical cuts DNA at every nucleotide, with the amount of cutting proportional to the solvent accessible surface area (SASA) of the deoxyribose hydrogen atoms. Cleavage fragments are quantified by a fluorescence sequencer, followed by normalization and deposition into the database. Our database currently contains 151 DNA sequences with lengths ranging from 35 to 41 nucleotides. These data have enabled us to develop some general rules regarding the sequence-dependence of DNA structure as well as to predict the cleavage pattern of any given DNA sequence with remarkable precision. Using this prediction algorithm, it is possible to construct structural maps of entire genomes. As there are many examples of DNA binding proteins with highly degenerate binding sites, the use of structural information to locate these sites may be helpful. There also exists other signals, including the signal for nucleosome positioning, which have no apparent consensus, making it likely that the structure of DNA is of critical importance. We have developed algorithms to identify regions of conserved structure using •OH cleavage intensity as a proxy. Within a set of DNase I hypersensitive sites (DHS) obtained from the ENCODE Consortium, we were able to identify a stretch of 12 nucleotides for which the structural conservation is much greater than the sequence conservation. These sites have been dubbed Conserved •OH Radical Cleavage Signatures, or CORCS. Upon further analysis, these CORCS were found to be 17-fold enriched for DHS as compared to shuffled elements. Through the continued analysis of hydroxyl radical cleavage data and development of algorithms to employ the data in biologically meaningful ways, we hope to further our understanding of the relationship between DNA sequence and structure, and how the local structural heterogeneity of genomic DNA contributes to biological function. / 2031-01-02

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Concern over the occurrence of micropollutants in drinking water and their health effects is increasing. Therefore, there is a growing interest in understanding micropollutant removal during drinking water treatment. Ozonation and advanced oxidation processes (AOPs) have been found to be effective in the degradation of many micropollutants. Ozonation involves reactions with both molecular ozone (direct pathway) and hydroxyl radicals (indirect pathway), while hydroxyl radicals are the main oxidants in advanced oxidation processes. Reaction rate constants of micropollutants with molecular ozone (kO3) and hydroxyl radicals (kOH) are indicators of their reactivity and are therefore useful in assessing their removal efficiency in ozonation and AOPs. However, to date, only a limited number of rate constants are available for micropollutants, especially emerging micropollutants such as endocrine disrupting chemicals (EDCs) and pharmaceuticals. Quantitative structure-property relationships (QSPR) are therefore desirable for predicting rate constants of numerous untested micropollutants without experimentation. The overall objective of this thesis was to develop predictive QSPR models which correlate the rate constants of a wide range of structural diverse micropollutants to their structural characteristics. To ensure the wide applicability of the QSPR models, the training set compound selection is critical and a group of heterogeneous compounds which are structurally representative of many others is preferred. A systematic compound selection approach which involves principal component analysis (PCA) and D-optimal onion design was applied for the first time in water treatment research. As a result, 22 micropollutants with diverse structures were selected as representatives from a large pool of micropollutants of interest (182 compounds). In addition, 12 molecular descriptors were identified which link relevant structural features to the removal mechanisms of oxidation processes. The kO3 and kOH values of the 22 selected micropollutants were then determined experimentally in bench-scale reactors at neutral pH using high performance liquid chromatography equipped with a photodiode array detector (HPLC-PDA). Three methods, competition kinetics, compound monitoring, and ozone monitoring were used for kO3 measurement, and competition kinetics was used for kOH measurement. As expected, kO3 values span a wide range from 10-2 to 107 M-1 s-1 because of the selective nature of molecular ozone. The general trends of micropollutant reactivity with ozone can be explained by the micropollutant structures and the electrophilic nature of ozone reactions. The kOH values range from 108 to 1010 M-1 s-1 because hydroxyl radicals are relatively non-selective in their reactions. For the majority of these micropollutants kO3 and kOH values were not reported prior to this study. Thus they provide valuable information for modeling and designing of ozonation and AOP treatment. QSPR models for kO3 and kOH prediction were then developed with special attention to model validation, applicability domain and mechanistic interpretation. With the experimentally determined rate constants, QSPR models were developed for predicting kO3 values using the selected 22 micropollutants as the training set and the 12 identified descriptors as model variables. As a result, two QSPR models were developed using piecewise linear regression (PLR) both showing an excellent goodness-of-fit. Model 1 was governed by average molecular weight and number of phenolic functional groups, and Model 2 was dominated by two principal components extracted from the descriptor matrix. The models were then validated using an external validation set collected from the literature, showing good predictive power of both models. Prior to applying these models to unknown micropollutants they need to be classified as high-reactive (logkO3 > 2 M-1 s-1) or low-reactive (logkO3  2 M-1 s-1), so that the appropriate submodel of the PLR can be applied. A classification function using linear discriminant analysis (LDA) was therefore developed which worked very well for both training and validation sets. With the help of additional compounds collected from the literature, and DRAGON molecular descriptors, a QSPR model for kOH prediction in the aqueous phase was developed using multiple linear regression. As a result, 7 DRAGON descriptors were found to be significant in modeling kOH, which related kOH of micropollutants to their electronegativity, polarizability, presence of double bonds and H-bond acceptors. The model fitted the training set very well and showed great predictive power as assessed by the external validation set. In addition, the model is applicable to a wide range of micropollutants. The model’s applicability domain was defined using a leverage approach. The main contributions of this thesis lie in the successful development of QSPR models for kO3 and kOH value prediction which, for the first time, can be used for a wide range of structurally diverse micropollutants. In addition, all QSPR models were externally validated to verify their predictive power, and the applicability domains were defined so that the applicability of the models to new compounds can be determined. Finally, the applicability of the model to natural water was explored by combining the QSPR models with the established Rct concept which predicts micropollutant removals during ozone treatment of natural water but requires kinetic data as input. Results show that the kinetic data from the QSPR model predictions worked well in the Rct model providing reliable estimations for most of the selected micropollutants. This approach can therefore be used in water treatment for initial assessment and estimation of ozonation efficiency.

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.

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.

The hydroxyl (OH) radical is a common intermediate species in any hydrogen- or hydrocarbon-based flame. Investigating OH at elevated temperatures and pressures is not a trivial task, and many considerations must be made to fully study the molecule. Shock tubes can provide the experimenter with a wide range of temperatures and pressures to investigate a variety of combustion characteristics including, but not limited to, OH kinetic profiles. Described in this dissertation is the diagnostic used to measure OH within a shock tube using UV absorption spectroscopy from an enhanced UV Xenon lamp passed through a spectrometer. OH absorption was made over a narrow range of wavelengths around 309.551 nm within the widely studied OH X→A ground vibrational transition region. Experiments have been performed in the shock-tube facility at Texas A&M University using this OH absorption diagnostic. A calibration mixture of stoichiometric H2/O2 diluted in 98% argon by volume was tested initially and compared with a well-known hydrogen-based kinetics mechanism to generate an absorption coefficient correlation. This correlation is valid over the range of conditions observed in the experiments at two pressures near 2 and 13 atm and temperatures from 1182 to 2017 K. Tests were completed using the absorption coefficient correlation on stoichiometric mixtures of methane, methane and water, ethane, ethylene, and acetylene to compare against a comprehensive, detailed chemical kinetics mechanism which considers up through C5 hydrocarbons. Measurements of methane show good agreement in peak OH formation and ignition delay time when compared with the mechanism. Improvements can be made in the shape of the methane-oxygen OH profile, and sensitivity and rate of production analyses were performed with the mechanism to identify key reactions for tuning. Similar results were found for methane-water-oxygen mixtures with no difference in profile shape or ignition delay time noted. There is room for improvement between the mechanism and measured values of OH for ethane-, ethylene-, and acetylene-based mixtures, although interesting pre-ignition features are nonetheless captured relatively well by the mechanism. Uncertainty in the measurement comes from the inherent noise in the photomultiplier tube signal and is ±25-150 ppm for the 2-atm experiments and ±6-25 ppm for the 13-atm experiments.

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Biomass burning aerosols play an important role in the chemistry and physics of the atmosphere and therefore, affect global climate. Biomass burning aerosols are generally aqueous and have a strong saccharidic component due to the combustion and pyrolysis of cellulose, a major component of foliar fuel. This class of aerosol is known to affect both the absorption and scatter of solar radiation. Also, biomass burning aerosols contribute to cloud formation through their action as cloud-condensation nuclei. Many questions exist about the chemical speciation and chemical aging of biomass burning aerosols and how this affects their atmospheric properties and ultimately, global climate. Also, knowledge of the chemical components of these aerosols is important in the search for chemical tracers that can give information about the point or regional source, fuel type, and age of a biomass burning aerosol parcel. Levoglucosan was chosen for these studies as a model compound for biomass burning aerosols because of its high measured concentrations in aerosol samples. Levoglucosan often dominates the aerosol composition by mass. In this dissertation, laboratory proxy systems were developed to study the solution-phase chemistry of levoglucosan with common atmospheric reactants found in biomass burning aerosols (i.e. H+, •OH). To mimic these natural conditions, acid chemistry was studied using sulfuric acid in water (pH=4.5). The hydroxyl radical (•OH) was produced by the Fenton reaction which consists of iron, hydrogen peroxide and acid (H2SO4) in aqueous solvent. For studies in aqueous sulfuric acid, oligomers of levoglucosan were measured by matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF-MS). A rational mechanism is proposed based on both the acid-catalyzed cationic ring-opening of levoglucosan and nucleophilic attack of ROH from levoglucosan on the hemi-acetal carbon to produce pyranose oligomers through the formation of glycosidic bonds. Oligomer formation is further supported by attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR). Reactions of levoglucosan with •OH produced from Fenton chemistry were studied in solution. Two modes of oligomerization (2000 u) were observed for reaction times between 1 and 7 days using MALDI-TOF-MS and laser desorption ionization (LDI) TOF-MS. Single-mass unit continuum mass distributions with dominant -2 u patterns were measured and superimposed by a +176/+162 u oligomer series. This latter oligomer pattern was attributed to a Criegee rearrangement (+14 u) of levoglucosan, initiated by •OH, forming a lactone (176 u). The acid-catalyzed reaction of any ROH from levoglucosan (+162 u) forms an ester through transesterification of the lactone functionality, whereupon propagation forms polyesters. Proposed products and chemical mechanisms are suggested as sources and precursors of humic-like substances (HULIS), which are known to possess a large saccharic component and are possibly formed from biomass burning aerosols. These products could also serve as secondary tracers, giving further information on the source and age of the aerosol.