Academic literature on the topic 'Secondary functionalized hydrocarbons'

Monoterpenes, comprising hydrocarbons, are the largest class of plant secondary metabolites and are commonly found in essential oils. Monoterpenes and their derivatives are key ingredients in the design and production of new biologically active compounds. This review focuses on selected aliphatic, monocyclic, and bicyclic monoterpenes like geraniol, thymol, myrtenal, pinene, camphor, borneol, and their modified structures. The compounds in question play a pivotal role in biological and medical applications. The review also discusses anti-inflammatory, antimicrobial, anticonvulsant, analgesic, antiviral, anticancer, antituberculosis, and antioxidant biological activities exhibited by monoterpenes and their derivatives. Particular attention is paid to the link between biological activity and the effect of structural modification of monoterpenes and monoterpenoids, as well as the introduction of various functionalized moieties into the molecules in question.

Abstract. Organic compounds emitted in the atmosphere are oxidized in complex reaction sequences that produce a myriad of intermediates. Although the cumulative importance of these organic intermediates is widely acknowledged, there is still a critical lack of information concerning the detailed composition of the highly functionalized secondary organics in the gas and condensed phases. The evaluation of their impacts on pollution episodes, climate, and the tropospheric oxidizing capacity requires modelling tools that track the identity and reactivity of organic carbon in the various phases down to the ultimate oxidation products, CO and CO2. However, a fully detailed representation of the atmospheric transformations of organic compounds involves a very large number of intermediate species, far in excess of the number that can be reasonably written manually. This paper describes (1) the development of a data processing tool to generate the explicit gas-phase oxidation schemes of acyclic hydrocarbons and their oxidation products under tropospheric conditions and (2) the protocol used to select the reaction products and the rate constants. Results are presented using the fully explicit oxidation schemes generated for two test species: n-heptane and isoprene. Comparisons with well-established mechanisms were performed to evaluate these generated schemes. Some preliminary results describing the gradual change of organic carbon during the oxidation of a given parent compound are presented.

The results of a DFT study of elementary acts, both catalytic transformations of alkanes on hydride-hydroxyl forms of Fe4O7 and NiFe3O7 clusters, and processes of hydrocarbons transformation on iron and nickel-oxide clusters without initially hydride-hydroxyl filling are presented. Homolytic scission of the C–H bonds of alkanes on the hydride-hydroxyl form of the Fe4O7 cluster is accompanied by the formation of alkyl radicals capable of biradicals recombination according to the singlet type. There is also an additional reaction direction, which is represented by a singlet intra-associative rearrangement generating alcohols chemisorbed with the iron atom of the Fe4O6 cluster. This reaction is irreversible, proceeds with a large exothermic effect of 45.90 kcal∙mol-1, sufficient to overcome the chemisorption bond and diffuse into the volume of the supercritical fluid. The calculated characteristics of the interaction of alkanes with an iron-positioned hydroxyl group indicate that the activation energies of the forward direction of elementary acts in the homologous series: primary and secondary C–H bonds, lie in the range of 30.91-32.74 kcal∙mol-1, that is, these reactions are not very selective and strongly endothermic, since the activation energies of the reverse directions of the corresponding elementary acts are in the range of 1.40-3.27 kcal∙mol-1. The transition in the homologous series from the primary and secondary C–H bonds of propane to the tertiary C–H bonds of isobutane significantly changes the activation specificity of the homolytic scission of C–H bonds. The relative activation energy of the forward direction of the reaction decreases by about 8.00 kcal∙mol-1. A reaction system with the participation of the nickel-iron-oxide cluster NiFe3O7 and propane has been studied quantum-chemically. The result of the interaction of these reagents is the formation of isopropyl alcohol (propan-2-ol), which is chemisorbed with the nickel atom of the NiFe3O6 cluster. This reaction is irreversible and proceeds with a large exothermic effect of 50.95 kcal∙mol-1. The energetics of this process qualitatively coincides with the activation characteristics of the second stage of methane transformation on the Fe4O6 cluster; however, in this case, the reaction is a one-stage. It is noted that when carrying out various SCF extraction processes, for example, during the purification and regeneration of nickel and iron oxide catalysts, it should be borne in mind that the use of a propane-butane mixture as a supercritical fluid can be accompanied by its saturation with heavier hydrocarbons of linear and branched structure and alcohols. However, in real technological SCF processes, it is realistic to select the optimal temperature and flow regime that minimizes this effect. In the presence of a pre-reaction complex involving the hydrogen bond of the hydroxyl group of the initial propylene glycol and the interstitial oxygen atom (Fe–O–Fe) of the Fe4O7 cluster, a one-stage reaction with the oxidation product 1-hydroxypropan-2-ol becomes possible. The Fe4O6 iron oxide cluster with four coordinated iron centers having a hydroxyl group bound to each of them interacts with propylene glycol to form 1-hydroxypropan-2-ol, and the Fe–OH and Fe–O–Fe cluster substructures are the oxidative centers. In this case, the product of the reaction is a water molecule chemisorbed on the iron center and a hydrogen atom chemisorbed on the Fe–O–Fe substructure. This reaction is extremely exothermic (Q = 62.55 kcal∙mol-1) and has a very low activation energy for the forward direction of the reaction. By the example of the described heterogeneous hydrate-dissociative effects involving metal oxide surfaces and simple or functionalized alkanes, it can be seen that it is the protonated and hydroxylated forms of metal oxide surfaces that are responsible for elementary acts related to supercritical water oxidation.

Speciated particle-phase organic nitrates (pONs) were quantified using online chemical ionization MS during June and July of 2013 in rural Alabama as part of the Southern Oxidant and Aerosol Study. A large fraction of pONs is highly functionalized, possessing between six and eight oxygen atoms within each carbon number group, and is not the common first generation alkyl nitrates previously reported. Using calibrations for isoprene hydroxynitrates and the measured molecular compositions, we estimate that pONs account for 3% and 8% of total submicrometer organic aerosol mass, on average, during the day and night, respectively. Each of the isoprene- and monoterpenes-derived groups exhibited a strong diel trend consistent with the emission patterns of likely biogenic hydrocarbon precursors. An observationally constrained diel box model can replicate the observed pON assuming that pONs (i) are produced in the gas phase and rapidly establish gas–particle equilibrium and (ii) have a short particle-phase lifetime (∼2–4 h). Such dynamic behavior has significant implications for the production and phase partitioning of pONs, organic aerosol mass, and reactive nitrogen speciation in a forested environment.

Abstract. Residential wood burning contributes significantly to the total atmospheric aerosol burden; however, large uncertainties remain in the magnitude and characteristics of wood burning products. Primary emissions are influenced by a variety of parameters, including appliance type, burner wood load and wood type. In addition to directly emitted particles, previous laboratory studies have shown that oxidation of gas phase emissions produces compounds with sufficiently low volatility to readily partition to the particles, forming significant quantities of secondary organic aerosol (SOA). However, relatively little is known about wood burning SOA and the effects of burn parameters on SOA formation and composition are yet to be determined. There is clearly a need for further study of primary and secondary wood combustion aerosols to advance our knowledge of atmospheric aerosols and their impacts on health, air quality and climate. For the first time, smog chamber experiments were conducted to investigate the effects of wood loading on both primary and secondary wood combustion products. Products were characterized using a range of particle and gas phase instrumentation, including an aerosol mass spectrometer (AMS). A novel approach for polycyclic aromatic hydrocarbon (PAH) quantification from AMS data was developed and results were compared to those from GC-MS analysis of filter samples. Similar total particle mass emission factors were observed under high and average wood loadings, however, high fuel loadings were found to generate significantly higher contributions of PAHs to the total organic aerosol (OA) mass compared to average loadings. PAHs contributed 15 ± 4% (mean ± 2 sample standard deviations) to the total OA mass in high load experiments, compared to 4 ± 1% in average load experiments. With aging, total OA concentrations increased by a factor of 3 ± 1 for high load experiments compared to 1.6 ± 0.4 for average load experiments. In the AMS, an increase in PAH and aromatic signature ions at lower m/z values, likely fragments from larger functionalized PAHs, was observed with aging. Filter samples also showed an increase in functionalized PAHs in the particles with aging, particularly oxidized naphthalene species. As PAHs and their oxidation products are known to have deleterious effects on health, this is a significant finding to aid in the mitigation of negative wood burning impacts by improving burner operation protocols.

Abstract. Residential wood burning contributes to the total atmospheric aerosol burden; however, large uncertainties remain in the magnitude and characteristics of wood burning products. Primary emissions are influenced by a variety of parameters, including appliance type, burner wood load and wood type. In addition to directly emitted particles, previous laboratory studies have shown that oxidation of gas-phase emissions produces compounds with sufficiently low volatility to readily partition to the particles, forming considerable quantities of secondary organic aerosol (SOA). However, relatively little is known about wood burning SOA, and the effects of burn parameters on SOA formation and composition are yet to be determined. There is clearly a need for further study of primary and secondary wood combustion aerosols to advance our knowledge of atmospheric aerosols and their impacts on health, air quality and climate. For the first time, smog chamber experiments were conducted to investigate the effects of wood loading on both primary and secondary wood combustion products. Products were characterized using a range of particle- and gas-phase instrumentation, including an aerosol mass spectrometer (AMS). A novel approach for polycyclic aromatic hydrocarbon (PAH) quantification from AMS data was developed and results were compared to those from GC-MS analysis of filter samples. Similar total particle mass emission factors were observed under high and average wood loadings; however, high fuel loadings were found to generate significantly higher contributions of PAHs to the total organic aerosol (OA) mass compared to average loadings. PAHs contributed 15 ± 4% (mean ±2 sample standard deviations) to the total OA mass in high-load experiments, compared to 4 ± 1% in average-load experiments. With aging, total OA concentrations increased by a factor of 3 ± 1 for high load experiments compared to 1.6 ± 0.4 for average-load experiments. In the AMS, an increase in PAH and aromatic signature ions at lower m / z values, likely fragments from larger functionalized PAHs, was observed with aging. Filter samples also showed an increase in functionalized PAHs in the particles with aging, particularly oxidized naphthalene species. As PAHs and their oxidation products are known to have deleterious effects on health, this is a noteworthy finding to aid in the mitigation of negative wood burning impacts by improving burner operation protocols.

ABSTRACTRibonucleic acids, often called a biological jack of all trades, contribute intimately to every aspect of gene expression, including the synthesis of other polypeptide biocatalysts. The fundamental importance of recurring structural motifs and the kinetics and energetics of the complex secondary and tertiary structure of RNA have been shown to be intimately linked with its functions in vivo. We have developed a novel enzymatic synthetic approach for covalent attachment of photoresponsive units into the RNA backbone. The synthetic conditions of this approach are extremely mild, involving the reverse micellar solubilization of nucleic acid along with lipase in apolar hydrocarbon solvents. Lipase catalyzed acylation of the 2' hydroxyl group in the ribose sugars of the RNA molecule has been used to incorporate photo-isomerizable azobenzene groups into the RNA strands. This micellar approach was envisaged for RNA functionalization while maintaining the conformational integrity of the macromolecular backbone in neutral buffer solution. The modification of RNA using covalently attached chromophores or fluorophores can be extended to other biomacromolecular matrices leading to the development of more versatile photoactive biopolymers. The photo-isomerizable groups incorporated in the RNA molecule can serve as optical ‘handles’ for the manipulation of the conformation of RNA and open new opportunities for biophotonic device applications.

Polar organic molecules are defined by differences in electronegativity between their atomic constituents and the resulting asymmetrical structures. They represent the basic chemical building blocks of life. Having a strong affinity to water (H[subscript]2O), which is essential for life on Earth, polar molecules are studied by the discipline of biochemistry and their origin, distribution, and function in living systems is relatively well understood. Polar constituents of sedimentary organic matter and petroleum have been previously studied but they are, in general, yet far from being understood. They can be present as primary biogenic molecules, rearranged biogenic molecules, or secondary functionalized hydrocarbons. The studies compiled in this thesis use selected polar organic compounds as molecular tools: phospholipids as indicators of biomass, high-molecular-weight polycyclic aromatic hydrocarbons as combustion markers, phenols as indicators of oil-water interaction processes, and carboxylic acids in general.Chapter 2 studies the biological oxidation of petroleum accumulations; a process mediated by microbes that inhabit the deep subsurface and affect the long-term storage of living carbon as sedimentary biomass of the ‘deep biosphere’. The results presented in chapter 2 suggest that intact bacterial cells are present in biodegraded petroleum, as indicated by the detection of membrane lipid fragments, termed phospholipids, in these oil samples. Carboxylic acids released from phospholipids (i.e. phospholipid fatty acids, PLFA) in oil samples vary in concentration (~2.0 - ~10.0 µg/g oil) and composition (i-C[subscript]14:0 dominated vs. i-C[subscript]15:0 and i-C[subscript]17:0 dominated) during progressive petroleum biodegradation, thereby showing that the microbial community increases in size during the removal of petroleum constituents, and that the community structure changes. Not one but at least two structurally different microbial consortia are shown to be responsible for petroleum degradation. Chapter 4 evaluates the rapid oxidation of biomass during the impact of an extraterrestrial bolide, which occurred during the late Neoproterozoic.The co-occurrence of a -3.5‰ negative sedimentary stable carbon isotope excursion and a molecular combustion-marker anomaly (coronene; 0.48 ppb, relative to a 0.04 ppb background), which are followed by a diversification of Acritarch species, suggests that combustion of ‘early’ terrestrial and marginallymarine biomass might have caused extensive smoke and atmospheric dimming, as well as subsequent photosynthetic stress. Moreover, the sharp combustion marker anomaly can probably provide a long-sought chronostratigraphic marker for the late Neoproterozoic, when also detected in other locations around the globe. Chapter 5 evaluates the effects of petroleum interaction with water. For this purpose oils produced from one reservoir were monitored during a 335-day period following the rationale that oil-water interaction increases during petroleum production. Based on a selective depletion of volatile aromatics and invariant phenol concentrations the results exclude both evaporative and oil-water partitioning processes. Petroleum compositional changes, recorded mainly in the low-molecular-weight aromatic and phenol fractions, were tentatively attributed to abiotic oxidation processes. Furthermore, methodological advances in the analysis of carboxylic acids of low molecular weight, evaluated for the execution of the other studies, are presented in chapter 4.Overall, the presented results shed more light on carbon export fluxes from different sedimentary carbon reservoirs by shedding new light on deep biosphere metabolism, elucidating the significance of the Neoproterozoic Acraman impact event, and contributing to our knowledge of petroleum destruction through its interaction with water in sedimentary basins. Moreover, they show that, in contrast to traditional belief, NSO compounds in oils and bitumens can form useful molecular tools to study questions in petroleum geochemistry, biogeochemistry, and palaeobiogeochemistry. Understanding the size of carbon reservoirs and fluxes on Earth, as well as the mechanisms that cause these carbon fluxes, can increase our appreciation of global biogeochemical cycling and, in turn, explain ecosystem dynamics, past evolutionary events, and predict future change of current climatic conditions.