Archean phosphorus recycling facilitated by ultraviolet radiation.

Of the six elements incorporated into the major polymers of life, phosphorus is the least abundant on a global scale [E. Anders, M. Ebihara, Geochim. Cosmochim. Acta 46, 2363-2380 (1982)] and has been described as the "ultimate limiting nutrient" [T. Tyrrell, Nature 400, 525-531 (1999)]. In the modern ocean, the supply of dissolved phosphorus is predominantly sustained by the oxidative remineralization/recycling of organic phosphorus in seawater. However, in the Archean Eon (4 to 2.5 Ga), surface waters were anoxic and reducing. Here, we conducted photochemical experiments to test whether photodegradation of ubiquitous dissolved organic phosphorus could facilitate phosphorus recycling under the simulated Archean conditions. Our results strongly suggest that organic phosphorus compounds, which were produced by marine biota (e.g., adenosine monophosphate and phosphatidylserine) or delivered by meteorites (e.g., methyl phosphonate) can undergo rapid photodegradation and release inorganic phosphate into solution under anoxic conditions. Our experimental results and theoretical calculations indicate that photodegradation of organic phosphorus could have been a significant source of bioavailable phosphorus in the early ocean and would have fueled primary production during the Archean eon.

Abundant phosphorus expected for possible life in Enceladus's ocean.

Saturn's moon Enceladus has a potentially habitable subsurface water ocean that contains canonical building blocks of life (organic and inorganic carbon, ammonia, possibly hydrogen sulfide) and chemical energy (disequilibria for methanogenesis). However, its habitability could be strongly affected by the unknown availability of phosphorus (P). Here, we perform thermodynamic and kinetic modeling that simulates P geochemistry based on recent insights into the geochemistry of the ocean-seafloor system on Enceladus. We find that aqueous P should predominantly exist as orthophosphate (e.g., HPO42-), and total dissolved inorganic P could reach 10-7 to 10-2 mol/kg H2O, generally increasing with lower pH and higher dissolved CO2, but also depending upon dissolved ammonia and silica. Levels are much higher than <10-10 mol/kg H2O from previous estimates and close to or higher than ∼10-6 mol/kg H2O in modern Earth seawater. The high P concentration is primarily ascribed to a high (bi)carbonate concentration, which decreases the concentrations of multivalent cations via carbonate mineral formation, allowing phosphate to accumulate. Kinetic modeling of phosphate mineral dissolution suggests that geologically rapid release of P from seafloor weathering of a chondritic rocky core could supply millimoles of total dissolved P per kilogram of H2O within 105 y, much less than the likely age of Enceladus's ocean (108 to 109 y). These results provide further evidence of habitable ocean conditions and show that any oceanic life would not be inhibited by low P availability.

Novel Insights from Clinical Practice Autologous Blood Patch Pleurodesis and Endobronchial Valves for Management of Persistent Air Leaks in Two Cases of Tuberculosis.

INTRODUCTION: Pulmonary infections, such as tuberculosis, can result in numerous pleural complications including empyemas, pneumothoraces with broncho-pleural fistulas, and persistent air leak (PAL). While definitive surgical interventions are often initially considered, management of these complications can be particularly challenging if a patient has an active infection and is not a surgical candidate. CASE PRESENTATION: Autologous blood patch pleurodesis and endobronchial valve placement have both been described in remedying PALs effectively and safely. PALs due to broncho-pleural fistulas in active pulmonary disease are rare, and we present two such cases that were managed with autologous blood patch pleurodesis and endobronchial valves. CONCLUSION: The two cases presented illustrate the complexities of PAL management and discuss the treatment options that can be applied to individual patients.

Anoxic photogeochemical oxidation of manganese carbonate yields manganese oxide.

The oxidation states of manganese minerals in the geological record have been interpreted as proxies for the evolution of molecular oxygen in the Archean eon. Here we report that an Archean manganese mineral, rhodochrosite (MnCO3), can be photochemically oxidized by light under anoxic, abiotic conditions. Rhodochrosite has a calculated bandgap of about 5.4 eV, corresponding to light energy centering around 230 nm. Light at that wavelength would have been present on Earth's surface in the Archean, prior to the formation of stratospheric ozone. We show experimentally that the photooxidation of rhodochrosite in suspension with light centered at 230 nm produced H2 gas and manganite (γ-MnOOH) with an apparent quantum yield of 1.37 × 10-3 moles hydrogen per moles incident photons. Our results suggest that manganese oxides could have formed abiotically on the surface in shallow waters and on continents during the Archean eon in the absence of molecular oxygen.

Effect of Ni2+, Zn2+, and Co2+ on green rust transformation to magnetite.

In this study, we investigated Ni2+, Zn2+, and Co2+ mineralogical incorporation and its effect on green rust transformation to magnetite. Mineral transformation experiments were conducted by heating green rust suspensions at 85 °C in the presence of Ni2+, Zn2+, or Co2+ under strict anoxic conditions. Transmission electron microscopy and powder X-ray diffraction showed the conversion of hexagonal green rust platelets to fine grained cubic magnetite crystals. The addition of Ni2+, Zn2+, and Co2+ resulted in faster rates of mineral transformation. The conversion of green rust to magnetite was concurrent to significant increases in metal uptake, demonstrating a strong affinity for metal sorption/co-precipitation by magnetite. Dissolution ratio curves showed that Ni2+, Zn2+, and Co2+ cations were incorporated into the mineral structure during magnetite crystal growth. The results indicate that the transformation of green rust to magnetite is accelerated by metal impurities, and that magnetite is a highly effective scavenger of trace metals during mineral transformation. The implications for using diagenetic magnetite from green rust precursors as paleo-proxies of Precambrian ocean chemistry are discussed.

RMG Database for Chemical Property Prediction.

The Reaction Mechanism Generator (RMG) database for chemical property prediction is presented. The RMG database consists of curated datasets and estimators for accurately predicting the parameters necessary for constructing a wide variety of chemical kinetic mechanisms. These datasets and estimators are mostly published and enable prediction of thermodynamics, kinetics, solvation effects, and transport properties. For thermochemistry prediction, the RMG database contains 45 libraries of thermochemical parameters with a combination of 4564 entries and a group additivity scheme with 9 types of corrections including radical, polycyclic, and surface absorption corrections with 1580 total curated groups and parameters for a graph convolutional neural network trained using transfer learning from a set of >130 000 DFT calculations to 10 000 high-quality values. Correction schemes for solvent-solute effects, important for thermochemistry in the liquid phase, are available. They include tabulated values for 195 pure solvents and 152 common solutes and a group additivity scheme for predicting the properties of arbitrary solutes. For kinetics estimation, the database contains 92 libraries of kinetic parameters containing a combined 21 000 reactions and contains rate rule schemes for 87 reaction classes trained on 8655 curated training reactions. Additional libraries and estimators are available for transport properties. All of this information is easily accessible through the graphical user interface at https://rmg.mit.edu. Bulk or on-the-fly use can be facilitated by interfacing directly with the RMG Python package which can be installed from Anaconda. The RMG database provides kineticists with easy access to estimates of the many parameters they need to model and analyze kinetic systems. This helps to speed up and facilitate kinetic analysis by enabling easy hypothesis testing on pathways, by providing parameters for model construction, and by providing checks on kinetic parameters from other sources.

Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation.

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. Most notably, 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 includes parallelization for faster model generation and a new molecule isomorphism approach to improve computational performance. RMG has also been updated to use Python 3, ensuring compatibility with the latest cheminformatics and machine learning packages. 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.

Tellurite Adsorption onto Bacterial Surfaces.

Tellurium (Te) is an emerging contaminant and its chemical transformation in the environment is strongly influenced by microbial processes. In this study, we investigated the adsorption of tellurite [Te(IV), TeO32-] onto the common soil bacterium Bacillus subtilis. Thiol-blocking experiments were carried out to investigate the role of cell surface sulfhydryl sites in tellurite binding, and extended X-ray absorption fine structure (EXAFS) spectroscopy was performed to determine the chemical speciation of the adsorbed tellurite. The results indicate that tellurite reacts with sulfhydryl functional groups in the extracellular polymeric substances (EPS) produced by B. subtilis. Upon binding to sulfhydryl sites in the EPS, the Te changes from Te-O bonds to Te-S coordination. Further analysis of the surface-associated molecules shows that the EPS of B. subtilis contain proteins. Removal of the proteinaceous EPS dramatically decreases tellurite adsorption and the sulfhydryl surface site concentration. These findings indicate that sulfhydryl binding in EPS plays a key role in tellurite adsorption on bacterial surfaces.

The role of cysteine in tellurate reduction and toxicity.

The tellurium oxyanion tellurate is toxic to living organisms even at low concentrations; however, its mechanism of toxicity is poorly understood. Here, we show that exposure of Escherichia coli K-12 to tellurate results in reduction to elemental tellurium (Te[0]) and the formation of intracellular reactive oxygen species (ROS). Toxicity assays performed with E. coli indicated that pre-oxidation of the intracellular thiol pools increases cellular resistance to tellurate-suggesting that intracellular thiols are important in tellurate toxicity. X-ray absorption spectroscopy experiments demonstrated that cysteine reduces tellurate to elemental tellurium. This redox reaction was found to generate superoxide anions. These results indicate that tellurate reduction to Te(0) by cysteine is a source of ROS in the cytoplasm of tellurate-exposed cells.

Sociodemographic Characteristics and Physical Activity in Patients with COPD: A 3-Month Cohort Study.

Decreased physical activity (PA) is associated with morbidity and mortality in COPD patients. In this secondary analysis of data from a 12-week longitudinal study, we describe factors associated with PA in COPD. Participants completed the Physical Activity Checklist (PAC) daily for a 7- to 8-day period. PA was measured monthly using the Physical Activity Scale for the Elderly (PASE). At three different time points, daily step count was measured for one week with an Omron HJ-720ITC pedometer. The 35 participants were primarily male (94%) and White (91%), with an average age of 66.5 years and FEV1 44.9% predicted. Common activities reported on the PAC were walking (93%), preparing a meal (89%), and traveling by vehicle (96%). PA measured by both PASE score (p = 0.01) and average daily step count (p = 0.04) decreased during follow-up. In repeated measures multivariable modeling, participants living with others had a higher daily step count (ß = 942 steps, p = 0.01) and better PASE scores (ß = 46.4, p < 0.001). Older age was associated with decreased step count (ß = -77 steps, p < 0.001) whereas White race was associated with lower PASE scores (ß = -55.4, p < 0.001) compared to non-White race. Other demographic factors, quality of life, and medications were not associated with PA. A better understanding of the role of social networks and social support may help develop interventions to improve PA in COPD.

Serendipitous Formation of Semiconducting Semi-Nindigo Indigoid by the Degradation of Diindolopyrrole.

We report the serendipitous discovery and synthesis of an indigoid "semi-Nindigo" (2) via oxidation of a diindolopyrrole (1). The reaction of 2 with BF3Et2O affords the borylated derivative (3). The electronic spectra of 2 and 3 possess intense long wave absorptions near 600 and 650 nm. Compound 3 is weakly emissive in the near-infrared. Thin-film OFETs fabricated with 1 and 2 both exhibited hole mobility of 10-5 and 10-3 cm2/(V s), respectively.

Nickel-Catalyzed Cross-Electrophile Reductive Couplings of Neopentyl Bromides with Aryl Bromides.

5-Cyanoimidazole was identified as an inexpensive ligand for nickel-catalyzed cross-electrophile couplings by screening a diverse set of pharmaceutical compound library. A strategic screening approach led to the discovery of this novel ligand, which was successfully applied in the preparation of various alkylated arene products with good to high yields. Furthermore, the properties of this ligand allowed expanding the scope of reductive couplings to challenging substrates, such as sterically hindered neopentyl halides, which are known to generate motifs that are prevalent in biologically active molecules.

Sulfone-Mediated SNAr Reaction as a Powerful Tool for the Synthesis of 4-Quinolinyl Ethers and More-Application to the Synthesis of HCV NS3/4a Protease Inhibitor BI 201420.

An efficient general methodology for the synthesis of 4-quinolinyl ethers is demonstrated via a highly reactive SNAr reaction of 4-quinolinyl sulfones with a range of structurally diversified 1°, 2°, and 3° alcohols with a wide substrate scope and high yields. By adapting this methodology, a convergent synthesis of a complex target of HCV NS3/4a protease inhibitor BI 201420 was accomplished.

Pressure-dependent kinetics of peroxy radicals formed in isobutanol combustion.

Bio-derived isobutanol has been approved as a gasoline additive in the US, 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, ß, 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 γ-isobutanol radical with O2 forms HO2 + isobutanal. The recombination of ß-isobutanol radical with O2 forms a stabilized hydroperoxy alkyl radical below 400 K, water + an alkoxy radical at higher temperatures, and HO2 + an alkene above 1200 K. The recombination of ß-isobutanol radical with O2 results in a mixture of products between 700-1100 K, forming acetone + formaldehyde + OH at lower temperatures and forming HO2 + 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.

Synthesis of stable isotope-labelled firocoxib.

Firocoxib (ML-1,785,713) is a nonsteroidal, potent, and selective COX-2 inhibitor, approved for the control of pain and inflammation associated with osteoarthritis in dogs and horses, as well as to control postoperative pain and inflammation in dogs. We employed a six-step synthesis to prepare firocoxib-[13 C6 ] in an overall yield of 35% from the commercially available bromobenzene-[13 C6 ]. The synthetic route involved the preparation of the key intermediate phenyl-13 C6 -methyl sulfide using cesium carbonate and S-methylthiourea sulfate under transition-metal free conditions. A two-step preparation of firocoxib-[13 C,2 H3 ] via the sulfinic acid derivative of firocoxib and methyl iodide-[13 C,2 H3 ] using the procedure of Gauthier and Yoshikawa was first undertaken. However, the deuterium atoms of the methyl sulfone undergo extensive exchange in aqueous media even at neutral pH. The isotope-labelled firocoxib is intended as an internal standard for bioanalyses of firocoxib from biological matrices.

Application of a Preformed Pd-BIDIME Precatalyst to Suzuki-Miyaura Cross-Coupling Reaction in Flow.

The application of a Buchwald's third generation palladacycle containing a dihydrobenzooxaphosphole-based ligand (e.g., BIDIME) was reported in the Suzuki cross-coupling reaction. Using flow technology, high yield and reproducible Suzuki cross-coupling reaction for one of our key intermediates was achieved with Pd loadings as low as 0.5 mol %. This continuous flow approach overcomes catalyst deactivation and scale dependence issues that can be a problem in some traditional batch-mode operations and responds to the challenge of improving process greenness.

Development of a Scalable, Chromatography-Free Synthesis of t-Bu-SMS-Phos and Application to the Synthesis of an Important Chiral CF3-Alcohol Derivative with High Enantioselectivity Using Rh-Catalyzed Asymmetric Hydrogenation.

A chromatography-free, asymmetric synthesis of the C2-symmetric P-chiral diphosphine t-Bu-SMS-Phos was developed using a chiral auxiliary-based approach in five steps from the chiral auxiliary in 36% overall yield. Separtion and recovery of the auxiliary were achieved with good yield (97%) to enable recycling of the chiral auxiliary. An air-stable crystalline form of the final ligand was identified to enable isolation of the final ligand by crystallization to avoid chromatography. This synthetic route was applied to prepare up to 4 kg of the final ligand. The utility of this material was demonstrated in the asymmetric hydrogenation of trifluoromethyl vinyl acetate at 0.1 mol % Rh loading to access a surrogate for the pharmaceutically relavent chiral trifluoroisopropanol fragment in excellent yield and enantiomeric excess (98.6%).

Adsorption of Methylmercury onto Geobacter bemidijensis Bem.

The anaerobic bacterium Geobacter bemidijensis Bem has the unique ability to both produce and degrade methylmercury (MeHg). While the adsorption of MeHg onto bacterial surfaces can affect the release of MeHg into aquatic environments as well as the uptake of MeHg for demethylation, the binding of MeHg to the bacterial envelope remains poorly understood. In this study, we quantified the adsorption of MeHg onto G. bemidijensis and applied X-ray absorption spectroscopy (XAS) to elucidate the mechanism of MeHg binding. The results showed MeHg adsorption onto G. bemidijensis cell surfaces was rapid and occurred via complexation to sulfhydryl functional groups. Titration experiments yielded cell surface sulfhydryl concentrations of 3.8 ± 0.2 µmol/g (wet cells). A one-site adsorption model with MeHg binding onto sulfhydryl sites provided excellent fits to adsorption isotherms conducted at different cell densities. The log K binding constant of MeHg onto the sulfhydryl sites was determined to be 10.5 ± 0.4. These findings provide a quantitative framework to describe MeHg binding onto bacterial cell surfaces and elucidate the importance of bacterial cells as possible carriers of adsorbed MeHg in natural aquatic systems.

Phenyl radical + propene: a prototypical reaction surface for aromatic-catalyzed 1,2-hydrogen-migration and subsequent resonance-stabilized radical formation.

The C9H11 potential energy surface (PES) was experimentally and theoretically explored because it is a relatively simple, prototypical alkylaromatic radical system. Although the C9H11 PES has already been extensively studied both experimentally (under single-collision and thermal conditions) and theoretically, new insights were made in this work by taking a new experimental approach: flash photolysis combined with time-resolved molecular beam mass spectrometry (MBMS) and visible laser absorbance. The C9H11 PES was experimentally accessed by photolytic generation of the phenyl radical and subsequent reaction with excess propene (C6H5 + C3H6). The overall kinetics of C6H5 + C3H6 was measured using laser absorbance with high time-resolution from 300 to 700 K and was found to be in agreement with earlier measurements over a lower temperature range. Five major product channels of C6H5 + C3H6 were observed with MBMS at 600 and 700 K, four of which were expected: hydrogen (H)-abstraction (measured by the stable benzene, C6H6, product), methyl radical (CH3)-loss (styrene detected), H-loss (phenylpropene isomers detected) and radical adduct stabilization. The fifth, unexpected product observed was the benzyl radical, which was rationalized by the inclusion of a previously unreported pathway on the C9H11 PES: aromatic-catalysed 1,2-H-migration and subsequent resonance stabilized radical (RSR, benzyl radical in this case) formation. The current theoretical understanding of the C9H11 PES was supported (including the aromatic-catalyzed pathway) by quantitative comparisons between modelled and experimental MBMS results. At 700 K, the branching to styrene + CH3 was 2-4 times greater than that of any other product channel, while benzyl radical + C2H4 from the aromatic-catalyzed pathway accounted for ∼10% of the branching. Single-collision conditions were also simulated on the updated PES to explain why previous crossed molecular beam experiments did not see evidence of the aromatic-catalyzed pathway. This experimentally validated knowledge of the C9H11 PES was added to the database of the open-source Reaction Mechanism Generator (RMG), which was then used to generalize the findings on the C9H11 PES to a slightly more complicated alkylaromatic system.

Modeling study of the anti-knock tendency of substituted phenols as additives: an application of the reaction mechanism generator (RMG).

This work presents kinetic modeling efforts to evaluate the anti-knock tendency of several substituted phenols if used as gasoline additives. They are p-cresol, m-cresol, o-cresol, 2,4-xylenol, 2-ethylphenol, and guaiacol. A detailed kinetic model was constructed to predict the ignition of blends of the phenols in n-butane with the help of reaction mechanism generator (RMG), an open-source software package. The resulting model, which has 1465 species and 27 428 reactions, was validated against literature n-butane ignition data in the low-to-intermediate temperature range. To rank the anti-knock tendency of the additives, engine-like simulations were performed in a closed adiabatic homogenous batch reactor with a volume history derived from the pressure profile of a real research octane number (RON) engine test. The ignition timings of the additive blends were compared to that of primary reference fuels (PRFs) to quantitatively predict the anti-knock ability. The model predictions agree well with experimental determinations of the changes in RON induced by the additives. This study explains the chemical mechanism by which methyl-substituted phenols increase RON, and demonstrates how fundamental chemical kinetics can be used to evaluate practical fuel additive performance.