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In chemical kinetics research, kinetic models containing hundreds of species and tens of thousands of elementary reactions are commonly used to understand and predict the behavior of reactive chemical systems. Reaction Mechanism Generator (RMG) is a software suite developed to automatically generate such models by incorporating and extrapolating from a database of known thermochemical and kinetic parameters. Here, we present the recent version 3 release of RMG and highlight improvements since the previously published description of RMG v1.0. One important change is that RMG v3.0 is now Python 3 compatible, which supports the most up-to-date versions of cheminformatics and machine learning packages that RMG depends on. Additionally, RMG can now generate heterogeneous catalysis models, in addition to the previously available gas- and liquid-phase capabilities. For model analysis, new methods for local and global uncertainty analysis have been implemented to supplement first-order sensitivity analysis. The RMG database of thermochemical and kinetic parameters has been significantly expanded to cover more types of chemistry. The present release also includes parallelization for reaction generation and on-the-fly quantum calculations, and a new molecule isomorphism approach to improve computational performance. Overall, RMG v3.0 includes many changes which improve the accuracy of the generated chemical mechanisms and allow for exploration of a wider range of chemical systems.

Organic peroxy radicals (RO2) are key intermediates in the oxidation of organic compounds in both combustion systems and the atmosphere. While many studies have focused on reactions of RO2 in specific applications, spanning a relatively limited range of reaction conditions, the generalized behavior of RO2 radicals across the full range of reaction conditions (temperatures, pressures, and NO levels) has, to our knowledge, never been explored. In this work, two simple model systems, n-propyl peroxy radical and γ-isobutanol peroxy radical, are used to evaluate RO2 fate using pressure-dependent kinetics. The fate of these radicals was modeled based on literature data over 250-1250 K, 0.01-100 bar, and 1 ppt to 100 ppm of NO, which spans the typical range of atmospheric and combustion conditions. Covering this entire range provides a broad overview of the reactivity of these species under both atmospheric and combustion conditions, as well as under conditions intermediate to the two. A particular focus is on the importance of reactions that were traditionally considered to occur in only one of the two sets of conditions: RO2 unimolecular isomerization reactions (long known to occur in combustion systems but only recently appreciated in atmospheric systems) and RO2 bimolecular reactions of RO2 with NO (thought to occur mainly in atmospheric systems and rarely considered in combustion chemistry).

Position-specific isotope analysis (PSIA) can aid in understanding the origins of molecules. Destructive PSIA requires a model to track isotope substitution through reaction pathways. We present a general method based on the Reaction Mechanism Generator software to construct quantitative kinetic models with atom-specific isotope tracking and kinetic isotope effects during thermal decomposition of model compounds. A propane mechanism produced with this method is compared to experiments. Without tuning kinetic or thermodynamic parameters to experimental data, the mechanism replicated, within experimental uncertainty, the relationship between the parent molecule's position-specific values and the fragments' enrichments. These isotope-specific models can serve as an in silico platform to quantitatively assess secondary isotopic reactions which can scramble position-specific enrichments, design and optimize experimental conditions, and test feasibility of PSIA for new compounds. The proposed methodology creates new opportunities for applications in isotope analysis for a range of chemical compounds. Keywords: Kinetic isotope effect; Symmetry; Degeneracy; Isotopologue; Enrichment; Automated mechanism generation, National Science Foundation (Grant 1122374)

Confusion over how to account for symmetry numbers when reactants are identical can cause significant errors in isotopic studies. An extraneous factor of 2 in the reaction symmetry number, as proposed in the literature, violates reaction equilibrium and causes huge enrichment errors in isotopic analysis. In actuality, no extra symmetry factor is needed with identical reactants.

Bio-derived isobutanol has been approved as a gasoline additive in the U.S., but our understanding of its combustion chemistry still has significant uncertainties. Detailed quantum calculations could improve model accuracy leading to better estimation of isobutanol’s combustion properties and its environmental impacts. This work examines 47 molecules and 38 reactions involved in the first oxygen addition to isobutanol’s three alkyl radicals located α, β, and γ to the hydroxide. Quantum calculations are mostly done at CCSD(T)-F12/cc-pVTZ-F12//B3LYP/CBSB7, with 1-D hindered rotor corrections obtained at B3LYP/6-31G(d). The resulting potential energy surfaces are the most comprehensive isobutanol peroxy networks published to date. Canonical transition state theory and a 1-D microcanonical master equation are used to derive high-pressure-limit and pressure-dependent rate coefficients, respectively. At all conditions studied, the recombination of α- isobutanol radical with O2 forms HO2 and isobutanal. The recombination of γ-isobutanol radical with O2 forms a stabilized hydroperoxy alkyl radical below 400 K, water and an alkoxy radical at higher temperatures, and HO2 and an alkene above 1200 K. The recombination of β-isobutanol radical with O2 results in a mixture of products between 700-1100 K, forming acetone, formaldehyde and OH at lower temperatures and forming HO2 and alkenes at higher temperatures. The barrier heights, high-pressure-limit rates, and pressure-dependent kinetics generally agree with the results from previous quantum chemistry calculations. Six reaction rates in this work deviate by over three orders of magnitude from kinetics in detailed models of isobutanol combustion, suggesting the rates calculated here can help improve modeling of isobutanol combustion and its environmental fate.

This perspective gives our views on general aspects and future directions of gas‐phase atmospheric chemical kinetic mechanism development, emphasizing on the work needed for the sustainable development of chemically detailed mechanisms that reflect current kinetic, mechanistic, and theoretical knowledge. Current and future mechanism development efforts and research needs are discussed, including software‐aided autogeneration and maintenance of kinetic models as a future‐proof approach for atmospheric model development. There is an overarching need for the evaluation and extension of structure‐activity relationships (SARs) that predict the properties and reactions of the many multifunctionalized compounds in the atmosphere that are at the core of detailed mechanisms, but for which no direct chemical data are available. Here, we discuss the experimental and theoretical data needed to support the development of mechanisms and SARs, the types of SARs relevant to atmospheric chemistry, the current status and limitations of SARs for various types of atmospheric reactions, the status of thermochemical estimates needed for mechanism development, and our outlook for the future. The authors have recently formed a SAR evaluation working group to address these issues.

The human gut microbiota controls factors that relate to human metabolism with a reach far greater than originally expected. Microbial communities and human (or animal) hosts entertain reciprocal exchanges between various inputs that are largely controlled by the host via its genetic make-up, nutrition and lifestyle. The composition of these microbial communities is fundamental to supply metabolic capabilities beyond those encoded in the host genome, and contributes to hormone and cellular signalling that support the dynamic adaptation to changes in food availability, environment and organismal development. Poor functional exchange between the microbial communities and their human host is associated with dysbiosis, metabolic dysfunction and disease. This review examines the biology of the dynamic relationship between the reciprocal metabolic state of the microbiota-host entity in balance with its environment (i.e. in healthy states), the enzymatic and metabolic changes associated with its imbalance in three well-studied diseases states such as obesity, diabetes and atherosclerosis, and the effects of bariatric surgery and exercise.

A single-step method allowing the measurement of 13C intramolecular distribution of butane isomers (n- and i-butane) from natural gas samples was developed. The method builds up on the one that has been developed for propane, using on-line pyrolysis followed by isotope analysis of the pyrolytic fragments. The isotopic filiation between n-butane and its pyrolytic fragments was elucidated using samples spiked with 13C on terminal positions. The isotopic filiation for i-butane could not be shown experimentally due to the lack of commercially available enriched i-butane. We thus used a recent model named Reaction Mechanism Generator (RMG) to assess the origin of the fragments arising from i-butane pyrolysis. Butanes from natural gas samples from the Carnarvon Basin (Australia) and the Arkoma Basin (USA) were analyzed. The results are consistent with a model for thermogenic natural gas generation and suggest that combined intramolecular isotope composition of propane and n-butane can be related to the gas maturity. In addition, the method allows the detection and shed light on the mechanism of n-butane and i-butane biodegradation in natural gas reservoirs.

With the rise in production of natural gas, there is increased interest in homogeneous partial oxidation (POX) to convert methane to syngas (CO + H2), ethene (C2H4) and acetylene (C2H2). In POX, polycyclic aromatic hydrocarbons (PAH) are important undesired byproducts. To improve the productivity of such POX processes, it is necessary to have an accurate chemical mechanism for methane-rich combustion including PAH. A new mechanism was created to capture the chemistry from C0 to C12, incorporating new information derived from recent quantum chemistry calculations, with help from the Reaction Mechanism Generator (RMG) software. For better estimation of kinetics and thermochemistry of aromatic species, including reactions through carbene intermediates, new reaction families and additional data from quantum chemistry calculations were added to RMG-database. Many of the rate coefficients in the new mechanism are significantly pressure-dependent at POX conditions. The new mechanism was validated against electron-ionization molecular beam mass spectrometry (EI-MBMS) data from a high-temperature flow reactor reported by Kohler et al. In this work quantification of additional species from those experiments is reported including phenylacetylene (C8H6), indene (C9H8), naphthalene (C10H8) and acenaphthylene (C12H8) at many temperatures for several feed compositions. Comparison of the experimental species concentration data and the new kinetic model is satisfactory; the new mechanism is generally more accurate than other published mechanisms. Moreover, because the new mechanism is composed of elementary chemical reaction steps instead of global fitted kinetics, pathway analysis of species could be investigated step-by-step to understand PAH formation. For methane-rich combustion, the most important routes to key aromatics are propargyl recombination for benzene, reactions of the propargyl radical with the phenyl radical for indene, and hydrogen abstraction acetylene addition (HACA) for naphthalene.

Critical laboratory results require prompt reporting to the attending physician, as they may indicate that a patient is in a life-threatening condition. Although this important subject has been covered in many publications, it needs more attention from our healthcare organizations, which have no official policy on the subject. Matching expectations between the doctor and the laboratory needs to be better defined.The aim of this work was to inform the community of doctors and laboratories about the multiple problems concerning the reporting of critical laboratory results, to create a platform for exchanging views and ideas, and to build an extensive infrastructure for developing a unified plan to address this important issue.We present the results of four years of experience of reporting critical laboratory values at the Meir Medical Center Laboratories. The idea leading this work was to present the relatively low rate of critical results reported by the laboratories in 2010, sharing the problems discovered while investigating the situation in depth, and presenting the solutions that enabled us to obtain the desired results within four years.Gradual implementation of these improvements resulted in critical value reporting increasing from 55% in 2010 to 95% currently.We suggest a model for improving critical laboratory values reporting based on our 4-year experience, which emphasizes: (1) The importance of selecting proper tests and values for critical results; (2) The significance of using technology and computerized measures to support the process; and (3) Developing quick procedures for monitoring and controlling the process.

This study was designed to investigate concurrently the psychological and hormonal changes at three critical points during in vitro fertilization (IVF) treatment. One hundred thirteen couples suffering from mechanical and unexplained infertility participated in the study and 23 of them conceived. Psychological evaluation included background questionnaires, Lubin's Depression Adjective Check List, and Spielberger's State Trait Anxiety inventory. Cortisol and prolactin levels were estimated by radioimmunoassay. The results showed that patients' anxiety and depression scores were significantly higher than the population norm. Psychological test scores and hormonal levels showed a similar pattern of change, increasing on oocyte retrieval day, decreasing on embryo transfer day, and rising again on pregnancy test day. Differences between these phases were generally significant. Differences in parameters' means between conceiving (C) and nonconceiving (NC) women were generally not significant. However, correlations between psychological measures and hormonal levels showed a clear disparity between C and NC women in the last phase. Whereas significant negative correlations were found in C patients, no relationship was found in NC patients. The findings suggest that success in IVF treatment may depend, in part, on differential modes of coping with anxiety and depression, involving hormonal or endorphin mediation.

Gas composition and temperature profiles for anthracite gasified in a combustion pot have been measured and shown to be in good agreement with prediction. The pot was refractory of 6.5″×15.5″ and bed depths were up to 4′ deep. Gasification was in air, and in steam up to 38.5% with oxygen enrichment up to 31%. Measurements confirmed that the initial temperature rise at the bottom of the bed was very steep, at about 1000°C/cm. Comparison with model predictions showed that: the gas-solid reaction in the combustion region was mainly endothermic reduction of CO 2 in a double film, with the main heat release in the ambient gas by reaction of CO to CO 2 ; and that the bed temperature in this region was maintained by radiation as the principal heat transfer mechanism in the bed. This double film mechanism replaces the single film assumption that is common to essentially all past theories of solid bed combustion. The model is otherwise similar to a prior construct (2) but with an improved solution procedure in which computation for the two parabolic differential equations starts at the boundary between the combustion and gasification regions. In other experimental results with computational agreement it is shown: that with sufficiently high or low velocity, the reaction zone exhibits classical blow-off and flashback; that bed depth has no significant effect on the reaction zone width; that the main effect of a deep bed is to act as a heat exchanger; and that the model presented is able to predict with good accuracy the temperature and composition profiles for a wide range of air rates and reactive gas compositions of air with steam and oxygen enrichment.

The interaction between the daily distribution of carbohydrates and frequent self-blood-glucose monitoring (SBGM) was studied in 13 pregnant women who had had diabetes for 4 to 19 years. Before and during SBGM, data were obtained on dietary history, daily blood glucose levels, and HbA1C. Optimal control was found with 3 main meals and 5 snacks. The total daily caloric intake decreased without change in the proportions of protein, fat, and carbohydrate. Consumption of starch increased, and that of simple sugars decreased. Although no changes were made in the daily amount of insulin, the women's diabetic control improved significantly.