SciCombinator

Discover the most talked about and latest scientific content & concepts.

Concept: Organic chemistry

255

Emissions of organic substances with potential toxicity to humans and the environment are a major concern surrounding the rapid industrial development in the Athabasca oil sands region (AOSR). Although concentrations of polycyclic aromatic hydrocarbons (PAHs) in some environmental samples have been reported, a comprehensive picture of organic contaminant sources, pathways, and sinks within the AOSR has yet to be elucidated. We sought to use a dynamic multimedia environmental fate model to reconcile the emissions and residue levels reported for three representative PAHs in the AOSR. Data describing emissions to air compiled from two official sources result in simulated concentrations in air, soil, water, and foliage that tend to fall close to or below the minimum measured concentrations of phenanthrene, pyrene, and benzo(a)pyrene in the environment. Accounting for evaporative emissions (e.g., from tailings pond disposal) provides a more realistic representation of PAH distribution in the AOSR. Such indirect emissions to air were found to be a greater contributor of PAHs to the AOSR atmosphere relative to reported direct emissions to air. The indirect pathway transporting uncontrolled releases of PAHs to aquatic systems via the atmosphere may be as significant a contributor of PAHs to aquatic systems as other supply pathways. Emission density estimates for the three PAHs that account for tailings pond disposal are much closer to estimated global averages than estimates based on the available emissions datasets, which fall close to the global minima. Our results highlight the need for improved accounting of PAH emissions from oil sands operations, especially in light of continued expansion of these operations.

Concepts: Petroleum, Polycyclic aromatic hydrocarbon, Organic chemistry, Hydrocarbon, Aromaticity, Naphthalene, Phenanthrene, Anthracene

70

The European high Alps are internationally renowned for their dairy produce, which are of huge cultural and economic significance to the region. Although the recent history of alpine dairying has been well studied, virtually nothing is known regarding the origins of this practice. This is due to poor preservation of high altitude archaeological sites and the ephemeral nature of transhumance economic practices. Archaeologists have suggested that stone structures that appear around 3,000 years ago are associated with more intense seasonal occupation of the high Alps and perhaps the establishment of new economic strategies. Here, we report on organic residue analysis of small fragments of pottery sherds that are occasionally preserved both at these sites and earlier prehistoric rock-shelters. Based mainly on isotopic criteria, dairy lipids could only be identified on ceramics from the stone structures, which date to the Iron Age (ca. 3,000-2,500 BP), providing the earliest evidence of this practice in the high Alps. Dairy production in such a marginal environment implies a high degree of risk even by today’s standards. We postulate that this practice was driven by population increase and climate deterioration that put pressure on lowland agropastoral systems and the establishment of more extensive trade networks, leading to greater demand for highly nutritious and transportable dairy products.

Concepts: Iron, Milk, Dairy, Organic chemistry, Pottery, Archaeology, Prehistory, Alps

58

Airborne chemicals in the indoor environment arise from a wide variety of sources such as burning fuels and cooking, construction materials and furniture, environmental tobacco smoke as well as outdoor sources. To understand the contribution of exhaled e-cigarette aerosol to the pre-existing chemicals in the ambient air, an indoor air quality study was conducted to measure volatile organic compounds (including nicotine and low molecular weight carbonyls), polycyclic aromatic hydrocarbons, tobacco-specific nitrosamines and trace metal levels in the air before, during and after e-cigarette use in a typical small office meeting room. Measurements were compared with human Health Criteria Values, such as indoor air quality guidelines or workplace exposure limits where established, to provide a context for potential bystander exposures. In this study, the data suggest that any additional chemicals present in indoor air from the exhaled e-cigarette aerosol, are unlikely to present an air quality issue to bystanders at the levels measured when compared to the regulatory standards that are used for workplaces or general indoor air quality.

Concepts: Measurement, Smoking, Tobacco, Tobacco smoking, Nicotine, Polycyclic aromatic hydrocarbon, Organic chemistry, Electronic cigarette

48

Reaction prediction remains one of the major challenges for organic chemistry and is a prerequisite for efficient synthetic planning. It is desirable to develop algorithms that, like humans, “learn” from being exposed to examples of the application of the rules of organic chemistry. We explore the use of neural networks for predicting reaction types, using a new reaction fingerprinting method. We combine this predictor with SMARTS transformations to build a system which, given a set of reagents and reactants, predicts the likely products. We test this method on problems from a popular organic chemistry textbook.

Concepts: Product, Chemical reaction, Chemistry, Organic reaction, Biochemistry, Sodium, Organic chemistry, Forecasting

44

To plan the syntheses of small organic molecules, chemists use retrosynthesis, a problem-solving technique in which target molecules are recursively transformed into increasingly simpler precursors. Computer-aided retrosynthesis would be a valuable tool but at present it is slow and provides results of unsatisfactory quality. Here we use Monte Carlo tree search and symbolic artificial intelligence (AI) to discover retrosynthetic routes. We combined Monte Carlo tree search with an expansion policy network that guides the search, and a filter network to pre-select the most promising retrosynthetic steps. These deep neural networks were trained on essentially all reactions ever published in organic chemistry. Our system solves for almost twice as many molecules, thirty times faster than the traditional computer-aided search method, which is based on extracted rules and hand-designed heuristics. In a double-blind AB test, chemists on average considered our computer-generated routes to be equivalent to reported literature routes.

Concepts: Chemical reaction, Organic synthesis, Chemistry, Artificial intelligence, Organic chemistry, Monte Carlo, Neural network, Artificial neural network

42

Small-molecule synthesis usually relies on procedures that are highly customized for each target. A broadly applicable automated process could greatly increase the accessibility of this class of compounds to enable investigations of their practical potential. Here we report the synthesis of 14 distinct classes of small molecules using the same fully automated process. This was achieved by strategically expanding the scope of a building block-based synthesis platform to include even Csp3-rich polycyclic natural product frameworks and discovering a catch-and-release chromatographic purification protocol applicable to all of the corresponding intermediates. With thousands of compatible building blocks already commercially available, many small molecules are now accessible with this platform. More broadly, these findings illuminate an actionable roadmap to a more general and automated approach for small-molecule synthesis.

Concepts: Protein, Organic compound, Biochemistry, Organic chemistry, Class, Social class, Small molecule, Accessibility

35

Wristbands are increasingly used for assessing personal chemical exposures. Unlike some exposure assessment tools, guidelines for wristbands, such as preparation, applicable chemicals, and transport and storage logistics, are lacking. We tested the wristband’s capacity to capture and retain 148 chemicals including polychlorinated biphenyls (PCBs), pesticides, flame retardants, polycyclic aromatic hydrocarbons (PAHs), and volatile organic chemicals (VOCs). The chemicals span a wide range of physical-chemical properties, with log octanol-air partitioning coefficients from 2.1 to 13.7. All chemicals were quantitatively and precisely recovered from initial exposures, averaging 102% recovery with relative SD ≤21%. In simulated transport conditions at +30 °C, SVOCs were stable up to 1 month (average: 104%) and VOC levels were unchanged (average: 99%) for 7 days. During long-term storage at -20 °C up to 3 (VOCs) or 6 months (SVOCs), all chemical levels were stable from chemical degradation or diffusional losses, averaging 110%. Applying a paired wristband/active sampler study with human participants, the first estimates of wristband-air partitioning coefficients for PAHs are presented to aid in environmental air concentration estimates. Extrapolation of these stability results to other chemicals within the same physical-chemical parameters is expected to yield similar results. As we better define wristband characteristics, wristbands can be better integrated in exposure science and epidemiological studies.Journal of Exposure Science and Environmental Epidemiology advance online publication, 26 July 2017; doi:10.1038/jes.2017.9.

Concepts: Epidemiology, Polycyclic aromatic hydrocarbon, Flame retardant, Organic chemistry, Volatile organic compound, Organic compounds, Polychlorinated biphenyl, Biphenyl

30

Arynes (aromatic systems containing, formally, a carbon-carbon triple bond) are among the most versatile of all reactive intermediates in organic chemistry. They can be ‘trapped’ to give products that are used as pharmaceuticals, agrochemicals, dyes, polymers and other fine chemicals. Here we explore a strategy that unites the de novo generation of benzynes-through a hexadehydro-Diels-Alder reaction-with their in situ elaboration into structurally complex benzenoid products. In the hexadehydro-Diels-Alder reaction, a 1,3-diyne is engaged in a [4+2] cycloisomerization with a ‘diynophile’ to produce the highly reactive benzyne intermediate. The reaction conditions for this simple, thermal transformation are notable for being free of metals and reagents. The subsequent and highly efficient trapping reactions increase the power of the overall process. Finally, we provide examples of how this de novo benzyne generation approach allows new modes of intrinsic reactivity to be revealed.

Concepts: Chemical reaction, Hydrogen, Chemistry, Carbon, Organic chemistry, In situ, Power

29

Atmospheric chemistry is fueled by a large annual influx of nonmethane volatile organic compounds (NMVOC). These compounds influence ozone formation, lead to secondary organic aerosol production, and play a significant role for the oxidizing capacity of the atmosphere. The anthropogenic NMVOC budget is considerably uncertain due to the diversity of urban emission sources. Here, we present comprehensive observations of urban NMVOC eddy covariance fluxes using a newly designed proton-transfer-reaction quadrupole interface time-of-flight mass spectrometer. We found emission fluxes of a surprisingly large pool of oxygenated NMVOCs (OVOCs) with an appreciable fraction of higher oxidized OVOCs that cannot be explained by known fast photochemical turnaround or current primary emission estimates. Measured OVOC/NMVOC bulk flux ratios are two to four times higher than inferred from aggregated anthropogenic emission inventories. Extrapolating these results would double the global anthropogenic NMVOC flux. In view of globally accelerating urbanization, our study highlights the need to reevaluate the influence of anthropogenic NMVOC on atmospheric chemistry, human health, and the climate system.

Concepts: Carbon dioxide, Climate, Chemistry, Carbon, Organic chemistry, Atmosphere, Volatile organic compound, Organic compounds

29

Fossil biomolecules from an endogenous source were previously identified in Cretaceous to Pleistocene fossilized bones, the evidence coming from molecular analyses. These findings, however, were called into question and an alternative hypothesis of the invasion of the bone by bacterial biofilm was proposed. Herewith we report a new finding of morphologically preserved blood-vessel-like structures enclosing organic molecules preserved in iron-oxide-mineralized vessel walls from the cortical region of nothosaurid and tanystropheid (aquatic and terrestrial diapsid reptiles) bones. These findings are from the Early/Middle Triassic boundary (Upper Roetian/Lowermost Muschelkalk) strata of Upper Silesia, Poland. Multiple spectroscopic analyses (FTIR, ToF-SIMS, and XPS) of the extracted “blood vessels” showed the presence of organic compounds, including fragments of various amino acids such as hydroxyproline and hydroxylysine as well as amides, that may suggest the presence of collagen protein residues. Because these amino acids are absent from most proteins other than collagen, we infer that the proteinaceous molecules may originate from endogenous collagen. The preservation of molecular signals of proteins within the “blood vessels” was most likely made possible through the process of early diagenetic iron oxide mineralization. This discovery provides the oldest evidence of in situ preservation of complex organic molecules in vertebrate remains in a marine environment.

Concepts: Protein, Oxygen, Amino acid, Collagen, Organic compound, Organic chemistry, Fossil, Dinosaur