Thesis (Ph. D.)--Washington State University. / Includes bibliographical references.

Isoprene is the dominant non-methane organic compound emitted by vegetation into the atmosphere, with a global emission rate of ~ 500 Tg yr-1. Its oxidation serves as a major source of ground level ozone in North America during the summer months. Despite the significant impact on tropospheric chemistry, questions remain concerning the detailed oxidation mechanism. The initial step in the mechanism is the addition of OH to form four distinct isomers. The relative branching between these isomers influences the distribution of the final products. I present a comprehensive investigation into the mechanistic details of early steps in the oxidation mechanism of unsaturated hydrocarbons in the troposphere and employ theoretical and experimental techniques. To understand the detailed kinetics of the initial OH addition to unsaturated hydrocarbons, I first present a model developed for the ethylene-OH system. I present the details of a robust two-transition state model. I extend the developed two-transition state model to the case of OH addition to isoprene. Excellent agreement with observed temperature and pressure dependent rate constants affords a high confidence level in understanding of the kinetics and in the calculated branching ratio of the initial OH addition step. I then focus attention on the subsequent reactivity of the OH-isoprene adducts. Until recently, all four of the OH-isoprene adducts were supposed to have reacted with O2 via addition to form alkylperoxy radicals. Previous computational results suggest that two of the OH-isoprene adducts undergo an intramolecular cyclic isomerization followed by hydrogen abstraction by O2 to form stable carbonyl compounds. I have synthesized photolytic precursors, presenting a novel approach to probe the subsequent reactivity of individual hydroxyalkyl radicals. Initial verification of the cyclic isomerization pathway involved synthesis of the photolytic precursor corresponding to the 1,3-butadiene-OH adduct. A culmination of theoretical and experimental techniques allowed verification of the cyclic isomerization pathway. I synthesized the photolytic precursor, which provided a single isoprene-OH adduct. Employing laser photolysis/laser induced fluorescence, time-dependent multiplexed mass spectrometry, velocity map ion imaging, and theoretical techniques, we present the full characterization of the reactivity of the single isoprene-OH adduct in the presence of O2.

Isoprene (2-methyl-1,3-butadiene) is the most abundant non-methane hydrocarbon mostly emitted from the trees and its oxidation by hydroxyl radical contributes significantly to the tropospheric ozone production. We investigate the development of a detailed predictive mechanism for isoprene oxidation using both theory and experiment. We have identified a novel cyclization pathway for the radicals formed by hydroxy radical (OH) addition to the inner carbons of isoprene. The pathway predicted that C5 carbonyl compounds are produced, and it may also provide information on the preference of sites for OH addition. The nitrite/nitrate isomerization is directly related to the competition between ozone production and radical termination and was investigated using variational RRKM theory coupled with the master equation. We find that the dominant fate of the β-hydroxy alkoxy radicals produced from the dissociation reaction of nitrite is a prompt dissociation, whereas δ-hydroxy radicals isomerize to form dihydroxy radicals. We have performed experiments using laser photolysis (LP)/ laserinduced fluorescence (LIF) spectroscopy to study the initial addition reaction of the hydroxyl radical to isoprene. The overall reaction rates were estimated from experiments conducted at various pressures and temperatures. The determined Arrhenius rates are k∞(T) = (3.49±0.46)x10-11exp(366±40)/T molecule-1 cm3 s-1 and k∞(T) = (3.58±0.18)x10- 11exp(356±18)/T molecule-1 cm3 s-1, for the OH and OD addition reactions, respectively. Isoprene oxidation in the presence of O2 and NO was studied and, based on simulations to OH cycling curves, we determined a value of (9.0±3.0)x10-12 molecule-1 cm3 s-1 for the overall reaction rate constant of hydroxy peroxy radical with NO at 298 K. We report a rate constant for O2 addition to the hydroxy alkyl radical of (2.3±2.0)x10-12 molecule-1 cm3 s-1 at 298 K. We find little generation of OH from the OD initiated oxidation of isoprene, and no significant differences in OH and OD cycling, which suggests that the H-shift isomerization is the major pathway for δ-hydroxy alkoxy radicals in agreement with theoretical predictions.

No description available.

The isoprenoid biosynthetic pathway (IBP) plays an important role in cellular metabolism. Currently there are drugs, including lovastatin and the nitrogenous bisphosphonates risedronate and zoledronate, that are used clinically to lower cholesterol levels and treat bone disease, respectively. These drugs work by inhibition of the upstream enzymes, HMG-CoA reductase and farnesyl diphosphate synthase (FDPS), respectively. The enzyme FDPS catalyzes the formation of farnesyl pyrophosphate (FPP), an important intermediate that represents a branch point in the pathway. The post-translational modification known as protein prenylation is mediated by the three prenyltransferase enzymes. Even though compounds like lovastatin, risedronate, and zoledronate indirectly disrupt protein prenylation, they also impair processes downstream from the point of inhibition. Therefore a direct approach would be desirable where downstream enzymes are targeted so that the rest of the cellular processes can continue to function. One such downstream enzyme is geranylgeranyl transferase II (GGTase II). This enzyme and it catalyzes the transfer of two hydrophobic geranylgeranyl chains from geranylgeranyl pyrophosphate (GGPP) to Rab proteins, which are essential for intracellular membrane trafficking. Inhibition of GGTase II may be a good therapeutic target for diseases such as multiple myeloma characterized by an over secretion of proteins. A known GGTase II inhibitor is the carboxy phosphonate 3-PEHPC, however millimolar concentrations are necessary to observe cellular effects with this compound. In an effort to develop more potent inhibitors of this enzyme, a family of isoprenoid triazole bisphosphonates was initially prepared by click chemistry, first as a mixture of olefin isomers due to an allylic azide rearrangement. These compounds were tested by our collaborators to determine the compounds’ activity as GGTase II inhibitors. Because some triazole bisphosphonates showed good activity as a mixture of isomers, a family of isoprenoid triazole bisphosphonates as single olefin isomers now has been prepared through the use of epoxy azides to avoid the azide rearrangement. The biological activity of these compounds has been studied and some of these triazole bisphosphonates were found to be potent and selective inhibitors of geranylgeranyl diphosphate synthase (GGDPS). While the enzyme GGDPS is upstream of the geranylgeranyltransferases, it is still downstream of the pathway’s primary branch point and provides GGPP for Rab geranylgeranylation. Two other families of triazole bisphosphonate analogues, homo- and bishomoisoprenoid triazole bisphosphonates, also have been prepared and tested by our collaborators to explore the compounds’ activity as GGDPS inhibitors, as well as the structure-activity-relationship. Previous research has shown digeranyl bisphosphonate (DGBP) and the bisphosphonate ether C-prenyl-O-geranyl bisphosphonate to be inhibitors of GGDPS. Two C-alkyl-C-homoalkyl DGBP analogues have been synthesized in order to study further the binding of these compounds to GGDPS, and dialkylated triazole bisphosphonates have been prepared to explore the effect of a triazole moiety on the analogue’s ability to inhibit GGDPS. The activity uncovered through these studies encourages further research on inhibitors of GGDPS.

The tropospheric oxidation of unsaturated hydrocarbons is a central issue in atmospheric chemistry. These hydrocarbons are emitted into the atmosphere from both natural and anthropogenic sources, and their atmospheric oxidation leads to different atmospheric pollutants, including ground level ozone, photochemical smog and secondary organic aerosols. Isoprene and 1,3-butadiene represent a biogenic and an anthropogenic hydrocarbon, respectively, which primarily undergo electrophilic addition of OH radical, followed by chain propagating radical reactions. Their oxidation is the major source for ground level ozone formation in both rural and urban area and understanding their chemistry is essential for regional air quality modeling. Until recently, most of the studies of isoprene chemistry have been non-isomer specific, reflecting the reactivity of combined pathways and therefore were insensitive to specific details of the isomeric pathways. An isomeric selective approach to studying unsaturated hydrocarbon oxidation is described in this dissertation. A synthesized precursor, whose photolysis can provide a route to the formation of energy selected single isomer in the isoprene oxidation pathway, enables the study of important channels that are difficult to unravel in non isomer specific experiments. The major addition channel in OH isoprene oxidation has been studied following the isomeric selective approach and using Laser Photolysis-Laser Induced Fluorescence (LP-LIF) as the primary experimental technique. The study reveals important information about the oxidative chemistry of the δ-peroxy radicals, accounting for about 20 percent of missing carbon balance in isoprene oxidation, and isomeric specific rate constants. A similar approach was applied to study the oxidation of 1,3-butadiene, and the photolytic precursor for the dominant hydroxy alkyl isomer in the OH initiated oxidation of 1,3-butadiene was synthesized. The subsequent experiments and analysis revealed detailed information about the oxidative chemistry accounting for approximately 26 percent of the missing chemistry. Finally, non isomeric selective OH cycling experiments were carried out on the1,3-butadiene system. By analyzing the OH cycling data with the combined information obtained from the isomeric specific studies of the two isomeric channels of 1,3-butadiene oxidation, the relative branching between the two isomeric channels of OH-1,3-butadiene oxidation was determined.

Thesis (M.S.)--Ohio University, November, 2002. / Title from PDF t.p. Includes bibliographical references (leaves 90-94)

In the continental United States, mean surface air temperature is expected to increase by up to 5°C within 100 years. With hotter temperatures, leaf budbreak is expected to occur earlier in forests, and leaf area is expected to increase in locations where temperature is limiting. The response of plant photosynthesis to hotter temperatures is less certain; plant productivity could increase or decrease. Past studies have found intraspecific variation in the responses of forest tree productivity, phenology, canopy leaf area, and leaf isoprene emission to warming, which all influence carbon uptake and yield for agricultural tree species; it is therefore important to understand not only how hot climates affect carbon uptake and biomass production between different tree species, but also in different genotypes of the same species. We conducted a common garden study at the Biosphere 2 research center near Oracle, AZ, USA. We created a hybrid poplar plantation of 168 trees, which were planted as cuttings in January 2013. The trees used in this study are comprised of 5 distinct genotypes of Populus deltoides × trichocarpa from a range of average annual air temperatures. We measured photosynthetic capacity, leaf phenological timing, canopy leaf area and aboveground woody biomass in 2014 growing season, and leaf isoprene emission in the 2015 growing season. We observed a strong effect of genotype on aboveground woody biomass increment, implying strong local adaptation to the home range and limited phenotypic plasticity in terms of physiological and biometric responses to high temperature environments. Our study suggests that genotypes from hotter home ranges are able to maintain photosynthetic capacity and canopy leaf area late into the growing season, despite high temperatures, and thus produce more aboveground woody biomass. This study may have implications for agricultural management—as temperatures warm where managers currently grow hybrid poplar for agricultural or other purposes, the genotypes from those home ranges would likely have reduced yield; managers could investigate the use of genotypes from home ranges with higher average temperatures to replace the vulnerable local varieties.

This work was a kinetic study of the Diels-Alder reaction of isoprene with variously substituted benzalmalononitriles. Application of the Hammett equation, a linear free energy relationship, to the kinetic rate data yielded a value of 1.31 for rho. This was interpreted as meaning the transition state for this Diels-Alder reaction was probably of the concerted type, although the nonconcerted polar transition state could not be eliminated in one case by the data of this study.Ball State UniversityMuncie, IN 47306

Isoprene is the most abundant volatile organic compound (VOC) emitted from vegetation, mainly trees. Because it plays an important role in tropospheric chemistry leading to formation of pollutants and enhancing the lifetime of the greenhouse gas methane, concern about the response of isoprene emissions to the rise in atmospheric CO2 concentration and global climate change has been increasing over the last few years. The consequences of predicted climate change will have complex repercussions on global isoprene emission. The increasing atmospheric CO2 per se will have direct effects on terrestrial vegetation since CO2 is the substrate of photosynthesis. Because photosynthesis is limited by CO2 at current ambient concentrations, an increase in CO2 is expected to increase leaf biomass (i.e. isoprene emitting surface). Predicted warmer climate, extended drought periods, the possible shift in plant species in favour of isoprene emitters and the increase in length of growing season, may cause an increase in global isoprene emissions with profound perturbations of air quality and the global carbon cycle. The aim of this thesis was to investigate the effect of environmental variables such as light, temperature, drought and leaf-to-air vapour pressure deficit (VPD), and the short- and long-term effect of atmospheric [CO2] on isoprene emission from temperate and tropical tree species. Both leaf and whole ecosystem level fluxes were studied. At the leaf scale, a short-term experiment with leaves of potted two-year old trees of Quercus virginiana was carried out, exposing plants to two drying-rewatering cycles. Leaf isoprene emission fell, but the process was considerably less sensitive to water stress than photosynthesis and stomatal conductance. In drought conditions, the large reduction in photosynthesis caused the percentage of fixed carbon lost as isoprene to increase as plants became more stressed, reaching peaks of 50% when photosynthesis was almost zero. Isoprene emissions also showed a strong negative linear relationship with pre-dawn leaf water potential (psi-leaf). In another experiment carried out at the large enclosed facility of Biosphere 2 (B2L, Arizona, USA), studying isoprene emission from leaves of three-year-old plants of Populus deltoides grown at three CO2 atmospheric concentrations (430, 800 and 1200 mu mol mol-1 CO2) in non-stressed conditions, instantaneous increases in atmospheric [CO2] always resulted in a reduction of isoprene emission and a stimulation of photosynthesis. Moreover, in the long-term, the CO2 inhibition effect for isoprene emission became a permanent feature for plants growing under elevated [CO2]. Again, isoprene emission was less responsive to drought than photosynthesis. Both water-stress and high VPD strongly stimulated isoprene emission and depressed photosynthetic rate as a result of stomatal closure and the resulting decreases in intercellular [CO2] (Ci). This also led to a dramatic increase in the proportion of assimilated carbon lost as isoprene. The effect of atmospheric elevated [CO2] and its interaction with high VPD and water stress on ecosystem gross isoprene production (GIP) and net ecosystem exchange of CO2 (NEE) in the Populus deltoides plantations was also studied. Although GIP and NEE showed a similar response to light and temperature, NEE was stimulated by elevated CO2 by 72% and depressed by high VPD, while GIP was inhibited by elevated CO2 by 58% and stimulated by high VPD. Similar to what was observed at leaf level, under water stress conditions GIP was stimulated in the short term and declined only when the stress was severe, whereas NEE started to decrease from the beginning of the experiment. This contrasting response led the percentage of assimilated carbon lost by the ecosystem as isoprene to increase as water stress progressed from 2.5% and 0.6% in well-watered conditions to 60% and 40% for the ambient and the elevated CO2 treatments, respectively. Again, we found water limitation and high VPD off-set the inhibitory effect of elevated CO2, leading to increased isoprene emissions. The effect of a mild water stress on GIP and gross primary production (GPP) was also observed in the model tropical rainforest mesocosm of B2L. Although GPP was reduced by 32% during drought, GIP was not affected and correlated very well with both light and temperature. The percentage of fixed C lost as isoprene tended to increase during drought because of the reduction in GPP. Consumption of isoprene by soil was observed in both systems. The isoprene sink capacity of litter-free soil of the agroforest stands showed no significant response to different CO2 treatments, while isoprene production was strongly depressed by elevated atmospheric [CO2]. In both mesocosms, drought suppressed the sink capacity, but the full sink capacity of dry soil was recovered within a few hours upon rewetting. In summary, elevated CO2 increased biomass production and photosynthesis while depressing isoprene production. However, both drought and VPD may off-set the CO2 effect and lead to enhanced isoprene emission. We conclude that the overall effect of global climate change could be of enhancing global isoprene emissions while depressing the soil sink, and that the soil uptake of atmospheric isoprene is likely to be modest but significant and needs to be taken into account for a comprehensive estimate of the global isoprene budget.