Trends in stabilisation of Criegee intermediates from alkene ozonolysis

Criegee Intermediates (CI), formed in the ozonolysis of alkenes, play a central role in tropospheric chemistry as an important source of radicals, with stabilised CI (SCI) able to participate in bimolecular reactions, affecting climate through the formation of inorganic and organic aerosol. However, total SCI yields have only been determined for a few alkene systems, while speciated SCI yields from asymmetrical alkenes are almost entirely unknown. Here we report for the first time a systematic experimental exploration of the stabilisation of CH2OO and (CH3)2COO CI, formed from ten alkene–ozone systems with a range of different sizes and structures, under atmospherically relevant conditions in the EUPHORE chamber. Experiments in the presence of excess SO2 (an SCI scavenger) determined total SCI yields from each alkene–ozone system. Comparison of primary carbonyl yields in the presence/absence of SO2 determined the stabilisation fraction of a given CI. The results show that the stabilisation of a given CI increases as the size of the carbonyl co-product increases. This is interpreted in terms of the nascent population of CI formed following decomposition of the primary ozonide (POZ) having a lower mean energy distribution when formed with a larger carbonyl co-product, as more of the energy from the POZ is taken by the carbonyl. These findings have significant implications for atmospheric modelling of alkene ozonolysis. Higher stabilisation of small CI formed from large alkenes is expected to lead to lower radical yields from CI decomposition, and higher SCI concentrations, increasing the importance of SCI bimolecular reactions

Kinetics of stabilised Criegee intermediates derived from alkene ozonolysis: reactions with SO2, H2O and decomposition under boundary layer conditions

The removal of SO2in the presence ofcis-but-2-ene and ozone exhibits a strong dependence on the water vapour concentration.</p

Rapid growth of HFC-227ea (1,1,1,2,3,3,3-Heptafluoropropane) in the atmosphere

We report the first measurements of 1,1,1,2,3,3,3-heptafluoropropane (HFC-227ea), a substitute for ozone depleting compounds, in remote regions of the atmosphere and present evidence for its rapid growth. Observed mixing ratios ranged from below 0.01 ppt in deep firn air to 0.59 ppt in the northern mid-latitudinal upper troposphere. Firn air samples collected in Greenland were used to reconstruct a history of atmospheric abundance. Year-on-year increases were deduced, with acceleration in the growth rate from 0.026 ppt per year in 2000 to 0.057 ppt per year in 2007. Upper tropospheric air samples provide evidence for a continuing growth until late 2009. Fur- thermore we calculated a stratospheric lifetime of 370 years from measurements of air samples collected on board high altitude aircraft and balloons. Emission estimates were determined from the reconstructed atmospheric trend and suggest that current "bottom-up" estimates of global emissions for 2005 are too high by more than a factor of three

Estimation of rate coefficients for the reactions of O3 with unsaturated organic compounds for use in automated mechanism construction

Reaction with ozone (O3) is an important removal process for unsaturated volatile organic compounds (VOCs) in the atmosphere. Rate coefficients for reactions of 3with VOCs are therefore essential parameters for chemical mechanisms used in chemistry transport models. Updated and extended structure-activity relationship (SAR) methods are presented for the reactions of O3 with mono- and polyunsaturated organic compounds. The methods are optimized using a preferred set of data including reactions of O3 with 221 unsaturated compounds. For conjugated dialkene structures, site-specific rates are defined, and for isolated polyalkenes rates are defined for each double bond to determine the branching ratios for primary ozonide formation. The information can therefore guide the representation of the O3 reactions in the next generation of explicit detailed chemical mechanisms

AtChem (version 1), an open-source box model for the Master Chemical Mechanism

AtChem is an open-source zero-dimensional box model for atmospheric chemistry. Any general set of chemical reactions can be used with AtChem, but the model was designed specifically for use with the Master Chemical Mechanism (MCM, http://mcm.york.ac.uk/, last access: 16 January 2020). AtChem was initially developed within the EUROCHAMP project as a web application (AtChem-online, https://atchem.leeds.ac.uk/webapp/, last access: 16 January 2020) for modelling environmental chamber experiments; it was recently upgraded and further developed into a stand-alone offline version (AtChem2), which allows the user to run complex and long simulations, such as those needed for modelling of intensive field campaigns, as well as to perform batch model runs for sensitivity studies. AtChem is installed, set up and configured using semi-automated scripts and simple text configuration files, making it easy to use even for inexperienced users. A key feature of AtChem is that it can easily be constrained to observational data which may have different timescales, thus retaining all the information contained in the observations. Implementation of a continuous integration workflow, coupled with a comprehensive suite of tests and version control software, makes the AtChem code base robust, reliable and traceable. The AtChem2 code and documentation are available at https://github.com/AtChem/ (last access: 16 January 2020) under the open-source MIT License

Improving together: better science writing through peer learning

Science, in our case the climate and geosciences, is increasingly interdisciplinary. Scientists must therefore communicate across disciplinary boundaries. For this communication to be successful, scientists must write clearly and concisely, yet the historically poor standard of scientific writing does not seem to be improving. Scientific writing must improve, and the key to long-term improvement lies with the early-career scientist (ECS). Many interventions exist for an ECS to improve their writing, like style guides and courses. However, momentum is often difficult to maintain after these interventions are completed. Continuity is key to improving writing. This paper introduces the ClimateSnack project, which aims to motivate ECSs to develop and continue to improve their writing and communication skills. The project adopts a peer-learning framework where ECSs voluntarily form writing groups at different institutes around the world. The group members learn, discuss, and improve their writing skills together. Several ClimateSnack writing groups have formed. This paper examines why some of the groups have flourished and others have dissolved. We identify the challenges involved in making a writing group successful and effective, notably the leadership of self-organized groups, and both individual and institutional time management. Within some of the groups, peer learning clearly offers a powerful tool to improve writing as well as bringing other benefits, including improved general communication skills and increased confidence

Newly detected ozone-depleting substances in the atmosphere

Ozone-depleting substances emitted through human activitiescause large-scale damage to the stratospheric ozone layer, and influence global climate. Consequently, the production of many of these substances has been phased out; prominent examples are the chlorofluorocarbons (CFCs), and their intermediate replacements, the hydrochlorofluorocarbons (HCFCs). So far, seven types of CFC and six types of HCFC have been shown to contribute to stratospheric ozone destruction 1,2. Here, we report the detection and quantification of a further three CFCs and one HCFC. We analysed the composition of unpolluted air samples collected in Tasmania between 1978 and 2012, and extracted from deep firn snow in Greenland in 2008, using gas chromatography with mass spectrometric detection. Using the firn data, we show that all four compounds started to emerge in the atmosphere in the 1960s. Two of the compounds continue to accumulate in the atmosphere. We estimate that, before 2012, emissions of all four compounds combined amounted to more than 74,000 tonnes. This is small compared with peak emissions of other CFCs in the 1980s of more than one million tonnes each year 2. However, the reported emissions are clearly contrary to the intentions behind the Montreal Protocol, and raise questions about the sources of these gases

Defining the ABC of gene essentiality in streptococci

Background Utilising next generation sequencing to interrogate saturated bacterial mutant libraries provides unprecedented information for the assignment of genome-wide gene essentiality. Exposure of saturated mutant libraries to specific conditions and subsequent sequencing can be exploited to uncover gene essentiality relevant to the condition. Here we present a barcoded transposon directed insertion-site sequencing (TraDIS) system to define an essential gene list for Streptococcus equi subsp. equi, the causative agent of strangles in horses, for the first time. The gene essentiality data for this group C Streptococcus was compared to that of group A and B streptococci. Results Six barcoded variants of pGh9:ISS1 were designed and used to generate mutant libraries containing between 33,000-66,000 unique mutants. TraDIS was performed on DNA extracted from each library and data were analysed separately and as a combined master pool. Gene essentiality determined that 19.5% of the S. equi genome was essential. Gene essentialities were compared to those of group A and group B streptococci, identifying concordances of 90.2% and 89.4%, respectively and an overall concordance of 83.7% between the three species. Conclusions The use of barcoded pGh9:ISS1 to generate mutant libraries provides a highly useful tool for the assignment of gene function in S. equi and other streptococci. The shared essential gene set of group A, B and C streptococci provides further evidence of the close genetic relationships between these important pathogenic bacteria. Therefore, the ABC of gene essentiality reported here provides a solid foundation towards reporting the functional genome of streptococci

An inter-laboratory comparison of urinary 3-hydroxypropylmercapturic acid measurement demonstrates good reproducibility between laboratories

<p>Abstract</p> <p>Background</p> <p>Biomarkers have been used extensively in clinical studies to assess toxicant exposure in smokers and non-smokers and have recently been used in the evaluation of novel tobacco products. The urinary metabolite 3-HPMA, a metabolite of the major tobacco smoke toxicity contributor acrolein, is one example of a biomarker used to measure exposure to tobacco smoke. A number of laboratories have developed liquid chromatography with tandem mass spectrometry (LC-MS/MS) based methods to measure urinary 3-HPMA; however, it is unclear to what extent the data obtained by these different laboratories are comparable.</p> <p>Findings</p> <p>This report describes an inter-laboratory comparison carried out to evaluate the comparability of 3-HPMA measurement between four laboratories. A common set of spiked and authentic smoker and non-smoker urine samples were used. Each laboratory used their in-house LC-MS/MS method and a common internal standard. A comparison of the repeatability ('r'), reproducibility ('R'), and coefficient of variation for 3-HPMA demonstrated that within-laboratory variation was consistently lower than between-laboratory variation. The average inter-laboratory coefficient of variation was 7% for fortified urine samples and 16.2% for authentic urine samples. Together, this represents an inter-laboratory variation of 12.2%.</p> <p>Conclusion</p> <p>The results from this first inter-laboratory comparison for the measurement of 3-HPMA in urine demonstrate a reasonably good consensus between laboratories. However, some consistent measurement biases were still observed between laboratories, suggesting that additional work may be required to further reduce the inter-laboratory coefficient of variation.</p