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SignificanceIn nature, plants and microbes process substantial amounts of aromatic carbon for lignin biosynthesis and breakdown, respectively. These natural processes have important implications in the pursuit of lignin valorization, which is crucial for a vibrant, global bioeconomy. In both plant and microbial systems, an open question remains regarding how lignin-related aromatic compounds are transported across compartmental membranes, either by active membrane transporters or via passive membrane crossing. In this study, we predict that passive transport processes in plants and bacteria for uncharged aromatic compounds are likely sufficient for lignin biosynthesis and catabolism, thus implying that membrane translocation rates are controlled by compound delivery and utilization rates and membrane concentration gradients. Lignin is an abundant aromatic polymer found in plant secondary cell walls. In recent years, lignin has attracted renewed interest as a feedstock for bio-based chemicals via catalytic and biological approaches and has emerged as a target for genetic engineering to improve lignocellulose digestibility by altering its composition. In lignin biosynthesis and microbial conversion, small phenolic lignin precursors or degradation products cross membrane bilayers through an unidentified translocation mechanism prior to incorporation into lignin polymers (synthesis) or catabolism (bioconversion), with both passive and transporter-assisted mechanisms postulated. To test the passive permeation potential of these phenolics, we performed molecular dynamics simulations for 69 monomeric and dimeric lignin-related phenolics with 3 model membranes to determine the membrane partitioning and permeability coefficients for each compound. The results support an accessible passive permeation mechanism for most compounds, including monolignols, dimeric phenolics, and the flavonoid, tricin. Computed lignin partition coefficients are consistent with concentration enrichment near lipid carbonyl groups, and permeability coefficients are sufficient to keep pace with cellular metabolism. Interactions between methoxy and hydroxy groups are found to reduce membrane partitioning and improve permeability. Only carboxylate-modified or glycosylated lignin phenolics are predicted to require transporters for membrane translocation. Overall, the results suggest that most lignin-related compounds can passively traverse plant and microbial membranes on timescales commensurate with required biological activities, with any potential transport regulation mechanism in lignin synthesis, catabolism, or bioconversion requiring compound functionalization.

pH is a fundamental aerosol property that affects ambient particle concentration and composition, linking pH to all aerosol environmental impacts. Here, PM1 and PM2. 5 pH are calculated based on data from measurements during the California Research at the Nexus of Air Quality and Climate Change (CalNex) study from 15 May to 15 June 2010 in Pasadena, CA. Particle pH and water were predicted with the ISORROPIA-II thermodynamic model and validated by comparing predicted to measured gas–particle partitioning of inorganic nitrate, ammonium, and chloride. The study mean ± standard deviation PM1 pH was 1.9 ± 0.5 for the SO42−–NO3−–NH4+–HNO3–NH3 system. For PM2. 5, internal mixing of sea salt components (SO42−–NO3−–NH4+–Na+–Cl−–K+–HNO3–NH3–HCl system) raised the bulk pH to 2.7 ± 0.3 and improved predicted nitric acid partitioning with PM2. 5 components. The results show little effect of sea salt on PM1 pH, but significant effects on PM2. 5 pH. A mean PM1 pH of 1.9 at Pasadena was approximately one unit higher than what we have reported in the southeastern US, despite similar temperature, relative humidity, and sulfate ranges, and is due to higher total nitrate concentrations (nitric acid plus nitrate) relative to sulfate, a situation where particle water is affected by semi-volatile nitrate concentrations. Under these conditions nitric acid partitioning can further promote nitrate formation by increasing aerosol water, which raises pH by dilution, further increasing nitric acid partitioning and resulting in a significant increase in fine particle nitrate and pH. This study provides insights into the complex interactions between particle pH and nitrate in a summertime coastal environment and a contrast to recently reported pH in the eastern US in summer and winter and the eastern Mediterranean. All studies have consistently found highly acidic PM1 with pH generally below 3.

A bstract In this article, building on our recent investigations and motivated by the fuzzball-paradigm, we explore normal modes of a probe massless scalar field in the rotating BTZ-geometry in an asymptotically AdS spacetime and correspondingly obtain the Spectral Form Factor (SFF) of the scalar field. In particular, we analyze the SFF obtained from the single-particle partition function. We observe that, a non-trivial Dip-Ramp-Plateau (DRP) structure, with a Ramp of slope one (within numerical precision) exists in the SFF which is obtained from the grand-canonical partition function. This behaviour is observed to remain stable close to extremality as well. However, at exact extremality, we observe a loss of the DRP-structure in the corresponding SFF. Technically, we have used two methods to obtain our results: (i) An explicit and direct numerical solution of the boundary conditions to obtain the normal modes, (ii) A WKB-approximation, which yields analytic, semi-analytic and efficient numerical solutions for the modes in various regimes. We further re-visit the non-rotating case and elucidate the effectiveness of the WKB-approximation in this case, which allows for an analytic expression of the normal modes in the regime where a level-repulsion exists. This regime corresponds to the lower end of the spectrum as a function of the scalar angular momentum, while the higher end of this spectrum tends to become flat. By analyzing the classical stress-tensor of the probe sector, we further demonstrate that the back-reaction of the scalar field grows fast as the angular momenta of the scalar modes increase in the large angular momenta regime, while the back-reaction remains controllably small in the regime where the spectrum has non-trivial level correlations. This further justifies cutting the spectrum off at a suitable value of the scalar angular momenta, beyond which the scalar back-reaction significantly modifies the background geometry.

Organic compounds and liquid water are major aerosol constituents in the southeast United States (SE US). Water associated with inorganic constituents (inorganic water) can contribute to the partitioning medium for organic aerosol when relative humidities or organic matter to organic carbon (OM ∕ OC) ratios are high such that separation relative humidities (SRH) are below the ambient relative humidity (RH). As OM ∕ OC ratios in the SE US are often between 1.8 and 2.2, organic aerosol experiences both mixing with inorganic water and separation from it. Regional chemical transport model simulations including inorganic water (but excluding water uptake by organic compounds) in the partitioning medium for secondary organic aerosol (SOA) when RH  >  SRH led to increased SOA concentrations, particularly at night. Water uptake to the organic phase resulted in even greater SOA concentrations as a result of a positive feedback in which water uptake increased SOA, which further increased aerosol water and organic aerosol. Aerosol properties, such as the OM ∕ OC and hygroscopicity parameter (κorg), were captured well by the model compared with measurements during the Southern Oxidant and Aerosol Study (SOAS) 2013. Organic nitrates from monoterpene oxidation were predicted to be the least water-soluble semivolatile species in the model, but most biogenically derived semivolatile species in the Community Multiscale Air Quality (CMAQ) model were highly water soluble and expected to contribute to water-soluble organic carbon (WSOC). Organic aerosol and SOA precursors were abundant at night, but additional improvements in daytime organic aerosol are needed to close the model–measurement gap. When taking into account deviations from ideality, including both inorganic (when RH  >  SRH) and organic water in the organic partitioning medium reduced the mean bias in SOA for routine monitoring networks and improved model performance compared to observations from SOAS. Property updates from this work will be released in CMAQ v5.2.

Mounting evidence from field and laboratory observations coupled with atmospheric model analyses shows that primary combustion emissions of organic compounds dynamically partition between the vapor and particulate phases, especially as near-source emissions dilute and cool to ambient conditions. The most recent version of the Community Multiscale Air Quality model version 5.2 (CMAQv5.2) accounts for the semivolatile partitioning and gas-phase aging of these primary organic aerosol (POA) compounds consistent with experimentally derived parameterizations. We also include a new surrogate species, potential secondary organic aerosol from combustion emissions (pcSOA), which provides a representation of the secondary organic aerosol (SOA) from anthropogenic combustion sources that could be missing from current chemical transport model predictions. The reasons for this missing mass likely include the following: (1) unspeciated semivolatile and intermediate volatility organic compound (SVOC and IVOC, respectively) emissions missing from current inventories, (2) multigenerational aging of organic vapor products from known SOA precursors (e.g., toluene, alkanes), (3) underestimation of SOA yields due to vapor wall losses in smog chamber experiments, and (4) reversible organic compounds–water interactions and/or aqueous-phase processing of known organic vapor emissions. CMAQ predicts the spatially averaged contribution of pcSOA to OA surface concentrations in the continental United States to be 38.6 and 23.6 % in the 2011 winter and summer, respectively. Whereas many past modeling studies focused on a particular measurement campaign, season, location, or model configuration, we endeavor to evaluate the model and important uncertain parameters with a comprehensive set of United States-based model runs using multiple horizontal scales (4 and 12 km), gas-phase chemical mechanisms, and seasons and years. The model with representation of semivolatile POA improves predictions of hourly OA observations over the traditional nonvolatile model at sites during field campaigns in southern California (CalNex, May–June 2010), northern California (CARES, June 2010), the southeast US (SOAS, June 2013; SEARCH, January and July, 2011). Model improvements manifest better correlations (e.g., the correlation coefficient at Pasadena at night increases from 0.38 to 0.62) and reductions in underprediction during the photochemically active afternoon period (e.g., bias at Pasadena from −5.62 to −2.42 µg m−3). Daily averaged predictions of observations at routine-monitoring networks from simulations over the continental US (CONUS) in 2011 show modest improvement during winter, with mean biases reducing from 1.14 to 0.73 µg m−3, but less change in the summer when the decreases from POA evaporation were similar to the magnitude of added SOA mass. Because the model-performance improvement realized by including the relatively simple pcSOA approach is similar to that of more-complicated parameterizations of OA formation and aging, we recommend caution when applying these more-complicated approaches as they currently rely on numerous uncertain parameters. The pcSOA parameters optimized for performance at the southern and northern California sites lead to higher OA formation than is observed in the CONUS evaluation. This may be due to any of the following: variations in real pcSOA in different regions or time periods, too-high concentrations of other OA sources in the model that are important over the larger domain, or other model issues such as loss processes. This discrepancy is likely regionally and temporally dependent and driven by interferences from factors like varying emissions and chemical regimes.

The implementation of stringent emission regulations has resulted in the decline of anthropogenic pollutants including sulfur dioxide (SO2), nitrogen oxides (NOx), and carbon monoxide (CO). In contrast, ammonia (NH3) emissions are largely unregulated, with emissions projected to increase in the future. We present real-time aerosol and gas measurements from a field study conducted in an agriculturally intensive region in the southeastern US during the fall of 2016 to investigate how NH3 affects particle acidity and secondary organic aerosol (SOA) formation via the gas–particle partitioning of semi-volatile organic acids. Particle water and pH were determined using the ISORROPIA II thermodynamic model and validated by comparing predicted inorganic HNO3-NO3- and NH3-NH4+ gas–particle partitioning ratios with measured values. Our results showed that despite the high NH3 concentrations (average 8.1±5.2 ppb), PM1 was highly acidic with pH values ranging from 0.9 to 3.8, and an average pH of 2.2±0.6. PM1 pH varied by approximately 1.4 units diurnally. Formic and acetic acids were the most abundant gas-phase organic acids, and oxalate was the most abundant particle-phase water-soluble organic acid anion. Measured particle-phase water-soluble organic acids were on average 6 % of the total non-refractory PM1 organic aerosol mass. The measured molar fraction of oxalic acid in the particle phase (i.e., particle-phase oxalic acid molar concentration divided by the total oxalic acid molar concentration) ranged between 47 % and 90 % for a PM1 pH of 1.2 to 3.4. The measured oxalic acid gas–particle partitioning ratios were in good agreement with their corresponding thermodynamic predictions, calculated based on oxalic acid's physicochemical properties, ambient temperature, particle water, and pH. In contrast, gas–particle partitioning ratios of formic and acetic acids were not well predicted for reasons currently unknown. For this study, higher NH3 concentrations relative to what has been measured in the region in previous studies had minor effects on PM1 organic acids and their influence on the overall organic aerosol and PM1 mass concentrations.

Partition coefficients describe the equilibrium partitioning of a single, defined charge state of a solute between two liquid phases in contact, typically a neutral solute. Octanol–water partition coefficients (Kow), or their logarithms (log P), are frequently used as a measure of lipophilicity in drug discovery. The partition coefficient is a physicochemical property that captures the thermodynamics of relative solvation between aqueous and nonpolar phases, and therefore provides an excellent test for physics-based computational models that predict properties of pharmaceutical relevance such as protein-ligand binding affinities or hydration/solvation free energies. The SAMPL6 Part II octanol–water partition coefficient prediction challenge used a subset of kinase inhibitor fragment-like compounds from the SAMPL6 pKa prediction challenge in a blind experimental benchmark. Following experimental data collection, the partition coefficient dataset was kept blinded until all predictions were collected from participating computational chemistry groups. A total of 91 submissions were received from 27 participating research groups. This paper presents the octanol–water log P dataset for this SAMPL6 Part II partition coefficient challenge, which consisted of 11 compounds (six 4-aminoquinazolines, two benzimidazole, one pyrazolo[3,4-d]pyrimidine, one pyridine, one 2-oxoquinoline substructure containing compounds) with log P values in the range of 1.95–4.09. We describe the potentiometric log P measurement protocol used to collect this dataset using a Sirius T3, discuss the limitations of this experimental approach, and share suggestions for future log P data collection efforts for the evaluation of computational methods.

Hydrogen is the main chemical component of the solar plasma, and H-ionization determines basic properties of the first adiabatic exponent Γ 1 . Its ionization significantly differs from the ionization of other chemicals. Due to the large number concentration, H-ionization causes a pronounced lowering of Γ 1 , with a strongly asymmetric and extending across almost the entire solar convective zone. The excited states in the hydrogen atom are modeled using a partition function, which accounts for the internal degrees of freedom of the composite particle. A temperature-dependent partition function with an asymptotic cut-off tail is derived from the quantum mechanical solution for the hydrogen atom in the plasma. We present numerical simulations of hydrogen ionization, calculated using two partition function models: Planck-Larkin (PL) and Starostin-Roerich (SR). In the SR model, the hydrogen ionization shifts to higher temperatures than in the PL model. Different models for excited states of the hydrogen atom may change Γ 1 by as much as 10 − 2 . The Γ 1 profiles for pure hydrogen exhibit a “twisted rope” structure for the two models, significantly affecting the helium ionization and the position of the helium hump. This entanglement of H and He effect provides a valuable opportunity to investigate the role of excited states in the solar plasma.

Comprehensive chlorine heterogeneous chemistry is incorporated into the Community Multiscale Air Quality (CMAQ) model to evaluate the impact of chlorine-related heterogeneous reaction on diurnal and nocturnal nitrate formation and quantify the nitrate formation from gas-to-particle partitioning of HNO3 and from different heterogeneous pathways. The results show that these heterogeneous reactions increase the atmospheric Cl2 and ClNO2 level (∼ 100 %), which further affects the nitrate formation. Sensitivity analyses of uptake coefficients show that the empirical uptake coefficient for the O3 heterogeneous reaction with chlorinated particles may lead to the large uncertainties in the predicted Cl2 and nitrate concentrations. The N2O5 uptake coefficient with particulate Cl− concentration dependence performs better in capturing the concentration of ClNO2 and nocturnal nitrate concentration. The reaction of OH and NO2 in the daytime increases the nitrate by ∼15 % when the heterogeneous chlorine chemistry is incorporated, resulting in more nitrate formation from HNO3 gas-to-particle partitioning. By contrast, the contribution of the heterogeneous reaction of N2O5 to nitrate concentrations decreases by about 27 % in the nighttime, when its reactions with chlorinated particles are considered. However, the generated gas-phase ClNO2 from the heterogeneous reaction of N2O5 and chlorine-containing particles further reacts with the particle surface to increase the nitrate by 6 %. In general, this study highlights the potential of significant underestimation of daytime concentrations and overestimation of nighttime nitrate concentrations for chemical transport models without proper chlorine chemistry in the gas and particle phases.

Toluene represents a large fraction of anthropogenic emissions and significantly contributes to tropospheric ozone and secondary organic aerosol (SOA) formation. Despite the fact that toluene is one of the most studied aromatic compounds, detailed chemical mechanisms still fail to correctly reproduce the speciation of toluene gaseous and condensed oxidation products. This study aims to elucidate the role of initial experimental conditions in toluene SOA mass loadings and to investigate gas–particle partitioning of its reaction products at different relevant temperatures. Gaseous and particulate reaction products were identified and quantified using a proton transfer reaction time-of-flight mass spectrometer (PTR-ToF-MS) coupled to a CHemical Analysis of aeRosol ONline (CHARON) inlet. The chemical system exhibited a volatility distribution mostly in the semi-volatile regime. Temperature decrease caused a shift of saturation concentration towards lower values. The CHARON–PTR-ToF-MS instrument identified and quantified approximately 60 %–80 % of the total organic mass measured by an aerosol mass spectrometer. A detailed mechanism for toluene gaseous oxidation was developed based on the Master Chemical Mechanism (MCM) and Generator for Explicit Chemistry and Kinetics of Organics in the Atmosphere (GECKO-A) deterministic mechanisms, modified following the literature. The new mechanism showed improvements in modeling oxidation product speciation with more observed species represented and more representative concentrations compared to the MCM–GECKO-A reference. Tests on partitioning processes, nonideality, and wall losses highlighted the high dependency of SOA formation on the considered processes. Our results underline the fact that volatility is not sufficient to explain the gas–particle partitioning: the organic and the aqueous phases need to be considered as well as the interactions between compounds in the particle phase.