Browsing by Subject "Photochemistry"
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Item Biological and photochemical degradation of dissolved organic carbon in peatland ecosystems.(2012-08) Jacobson, Meghan McCarthy FunkeApproximately one half of terrestrial carbon runoff is processed by inland waters and released into the atmosphere as carbon dioxide (CO2) prior to reaching the oceans, and bacterial consumption of dissolved organic carbon (DOC) comprises a dominant proportion of this carbon loss. Though peatlands export more DOC per area than most other ecosystems, the sources and biodegradability of peatland DOC and their effects on downstream DOC loads and fluxes are poorly understood. Moreover, photochemical degradation plays an important role in the loss of carbon from aquatic ecosystems, especially in peatlands with high DOC concentrations rich in photochemically reactive humic and phenolic compounds, but its contribution to global CO2 evasion from inland waters has not been quantified. This dissertation focuses on predictors of biodegradable DOC (BDOC) in aquatic ecosystems, the sources and biodegradability of DOC in peatland watersheds, and the contribution of photochemical degradation of DOC to global CO2 evasion from peatlands and fluvial ecosystems. Key findings from these studies were that SUVA, a measurement broadly used in ecology and environmental engineering and fairly simple to obtain, is an excellent predictor of the amount of long-term BDOC concentrations in Minnesota lake ecosystems. The peatland bog may be the most important source of BDOC exported from peatlands annually, rather than the upland. And, photochemical enhancement of bacterial respiration in peatland and fluvial ecosystems contributes approximately 0.11-0.22 Pg C yr-1 to the total global CO2 evasion from inland waters (~1.4 Pg C yr-1), or 9-18% of all inland water CO2 evasion. The results from this dissertation will lend insight into how future changes in hydrology and surface water DOC concentrations will alter the sources, biodegradability, and photochemical enhancement of DOC in aquatic ecosystems in the northern hemisphere, especially peatlands.Item Electronic Structure Method Development for Excited-State Chemistry(2017-09) Hoyer, ChadThe accurate modeling of photochemistry requires robust dynamics simulations on correct potential surfaces. A pragmatic approach is to first compute potential surfaces with an accurate electronic structure method, fit the surfaces to an analytic function, and then run dynamics using the fitted surfaces. This approach will be referred to as fitted dynamics. The focus of this work is on the electronic structure aspect of fitted dynamics. Specifically, I will discuss my work on benchmarking and method development of multiconfiguration pair-density functional theory (MC-PDFT) and diabatization method development. MC-PDFT is very similar to Kohn-Sham Density Functional Theory (KS-DFT); however, MC-PDFT uses a multiconfigurational (MC) wave function (WF) instead of a single Slater determinant (SD), the MC-PDFT energy is a functional of the den- sity and on-top pair density instead of only the density, and the MC-PDFT energy is computed via post-SCF instead of optimizing the molecular orbitals (MOs). Due to the MC nature of excited states, MC-PDFT is a promising alternative to KS-DFT for photochemistry. To check if MC-PDFT is useful for photochemistry, we first bench- marked it on vertical excitation energies of atoms and organic molecules. We found that MC-PDFT exhibits quantitative accuracy. We have also explored new theory developments, which may be of use for practical photochemistry applications. With regards to diabatization, the dipole-quadrupole (DQ) and dipole-quadrupole- electrostatic-potential (DQ ) diabatization schemes were developed. They diabatize using simple one-electron properties and the methods exhibit applicability to general systems.Item New Developments in Solid Phase Peptide Chemistry Facilitate the Study of the Unique Metalloprotease, Ste24(2023-03) Bader, TaysirProtein and peptide prenylation is an essential biological process involved in many signal transduction pathways. In its most prevalent form, prenylation involves three enzymatic steps; transfer of an isoprenoid moiety by FTase or GGTaseI to the cysteine of a C-terminal CaaX sequence (where C is cysteine, a is an aliphatic amino acid, and X is a variable amino acid dictating whether a farnesyl or longer geranylgeranyl chain is added), proteolytic removal of the aaX sequence by ZMPSTE24 or RCE1, and finally carboxymethylation of the newly exposed C-terminal cysteine by ICMT enzyme. ZMPSTE24 also catalyzes a second cleavage step upstream of the CaaX site in prelamin A, and mutations abolishing this step lead to progeroid diseases. Ste24 is the yeast homolog of ZMPSTE24 and is the founding member of a unique class of integral membrane metalloproteases. Its precise mechanism of action has yet to be explored fully at the molecular level, and it is unique in that it performs two separate cleavage reactions sequentially at distinct sites in the same substrate molecule. The system historically used for studying prenylation is the mating pheromone a-Factor, a dodecameric peptide with a methyl ester C-terminal farnesylated cysteine. Producing this and other prenylated peptides presents four key challenges: the C-terminal cysteine is prone to epimerization, the terminal methyl ester is not readily available through traditional SPPS, the terminal cysteine has to be chemoselectively modified with a hydrophobic prenyl chain on the C-terminal cysteine, and often there are several cysteines in the sequence which necessitates additional orthogonal protecting group chemistry. In this work, various synthetic methodologies were developed in order to overcome these challenges, and then utilized for the production of a myriad of peptide probes based on the structure of a-Factor. These probes were used to study both cleavage steps of ZMPSTE24, as well as the other enzymes involved in the prenylation pathway.Item Photochemical Studies: Method Development And Evaluation(2020-03) Parker, KelseyPhotochemistry is an important area of research, but modeling photochemical systems is complex and expensive. In this dissertation, I present my work on the testing and development of methods for photochemistry studies. Chapter 1 introduces some important concepts. In Chapter 2, I present an electronic structure method for excited states called the dual-functional Tamm-Dancoff approximation. This method is based on the relatively inexpensive time-dependent density functional theory (TDDFT) and it gives similar results to TDDFT away from conical intersection seams (CISs). Near CISs involving the ground state, DF-TDA shows an improvement over TDDFT because it gives the correct (F-2)-dimensionality of these seams, where F is the number of degrees of freedom of the potential energy surfaces. In Chapters 3 and 4, I present work on two diabatization methods for coupled electronic states: the dipole, quadrupole, electrostatic potential method and the N/D method. Neither method requires a user to define diabatic molecular orbitals, and both solve for diabatic energies without relying on following a path through coordinate space. Both methods are shown to be successful for a wide range of test cases. In Chapter 5, I present work on a method called extended Hamiltonian molecular dynamics, which is designed to be an inexpensive way to cut back on zero point energy leakage. I present our findings that this method is successful for several small test systems. Finally in Chapter 6, I present work on the construction of potential energy surfaces suitable for studying the photodissociation of methylamine. This work involves diabatization and a method called anchor points reactive potential, which is a multiscale method designed for making analytic representations of high-dimensional potential energy surfaces. My work on methylamine involves the extension of this method to a more complex system than it has previously been applied to, and I compare my surfaces to previous theoretical and experimental results and find good agreement. A theme of all this work is improving our understanding of photochemistry and designing methods to model these systems that are cost effective and generally applicable.Item Photodegradation of Natural Organic Matter in Plume Versus Non-plume Waters in Lake Superior(2021-08) Edge, DevinNatural organic matter (NOM) undergoes direct and indirect photodegradation under ultraviolet (UV) light exposure, is an important source of energy for the aquatic food web and affects how much light can penetrate a water column. Photodegradation of NOM can lead to photobleaching of colored dissolved organic matter (CDOM), the release of low-molecular weight (LMW) organic species and the release of bioavailable nitrogen and phosphorus species . Photomineralization of NOM can produce carbon dioxide and carbon monoxide, removing organic carbon from the system. Recent storm events of greater intensities and frequencies have caused increased amounts of runoff, including dissolved and particulate natural organic matter, in the Laurentian Great Lakes region. This increased runoff may change the extent and types photochemistry happening in surface waters of these large lakes. The differences between the photodegradation of natural organic matter from plume-impacted water versus open lake water in Lake Superior were studied by performing irradiations under natural sunlight at 47°N latitude in August and September 2020. Terrestrially impacted samples (both before and after a storm), as well as open water samples were exposed to three days of natural sunlight. Autoclaved whole-water and filtered-water samples from before, during, and after the irradiations, along with matching dark controls, were analyzed for total and dissolved organic carbon, total and dissolved nitrogen, total and dissolved phosphorus, soluble reactive phosphorus, ammonia, and UV-Visible spectroscopy proxies (spectral slope ratios, CDOM absorbance, and SUVA254). Irradiated filtered water samples from the terrestrially impacted and storm-impacted sites exhibited larger percent and overall changes in spectral slope ratios and greater losses of colored dissolved organic matter (CDOM) absorbance relative to open water samples. This differed from the whole water samples, where the storm-impacted site experienced the smallest percent change in UV-Vis measurements, most likely because the particulates in this sample limited its light exposure. Except for this site, filtered water irradiations generally experienced lower percent changes and overall changes in UV-Vis measurements compared to whole water samples. An increase in DOC concentration was found in the dark sample for the whole water irradiation of the terrestrially-impacted site taken before a storm occurred, indicating potential desorption occurring when POM is included. Finally, there was also an increase in ammonium concentration in the same aforementioned whole water sample upon light exposure. The photodegradation of organic matter in Lake Superior was mainly affected by site location and whole vs. filtered treatment, and resulted in some ammonium release in whole, terrestrially-impacted samples.