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Carbonyl sulfide (OCS) is a non-hygroscopic trace species in the free troposphere and the primary sulfur reservoir maintained by direct oceanic, geologic, biogenic and anthropogenic emissions and t...

Emissions of C 2 -C 5 alkanes from the U.S. oil and gas sector have changed rapidly over the last decade. We use a nested GEOS-Chem simulation driven by updated 2011NEI emissions with aircraft, surface, and column observations to (1) examine spatial patterns in the emissions and observed atmospheric abundances of C 2 -C 5 alkanes over the United States and (2) estimate the contribution of emissions from the U.S. oil and gas industry to these patterns. The oil and gas sector in the updated 2011NEI contributes over 80% of the total U.S. emissions of ethane (C 2 H 6 ) and propane (C 3 H 8 ), and emissions of these species are largest in the central United States. Observed mixing ratios of C 2 -C 5 alkanes show enhancements over the central United States below 2 km. A nested GEOS-Chem simulation underpredicts observed C 3 H 8 mixing ratios in the boundary layer over several U.S. regions, and the relative underprediction is not consistent, suggesting C 3 H 8 emissions should receive more attention moving forward. Our decision to consider only C 4 -C 5 alkane emissions as a single lumped species produces a geographic distribution similar to observations. Due to the increasing importance of oil and gas emissions in the United States, we recommend continued support of existing long-term measurements of C 2 -C 5 alkanes. We suggest additional monitoring of C 2 -C 5 alkanes downwind of northeastern Colorado, Wyoming, and western North Dakota to capture changes in these regions. The atmospheric chemistry modeling community should also evaluate whether chemical mechanisms that lump larger alkanes are sufficient to understand air quality issues in regions with large emissions of these species., SCOPUS: ar.j, info:eu-repo/semantics/published

TROPOMI (the TROPOspheric Monitoring Instrument), on-board the Sentinel-5 Precursor satellite, has been monitoring the Earth's atmosphere since October 2017, with an unprecedented horizontal resolution (initially 7×3.5 km2, upgraded to 5.5×3.5 km2 since August 2019). Monitoring air quality is one of the main objectives of TROPOMI, with the measurements of important pollutants such as nitrogen dioxide, carbon monoxide, and formaldehyde (HCHO). In this paper we assess the quality of the latest HCHO TROPOMI products (version 1.1.[5-7]), using ground-based solar-absorption FTIR (Fourier Transform Infrared) measurements of HCHO from twenty-five stations around the world, including high, mid, and low latitude sites. Most of these stations are part of the Network for the Detection of Atmospheric Composition Change (NDACC), and they provide a wide range of observation conditions from very clean remote sites to those with high HCHO levels from anthropogenic or biogenic emissions. The ground-based HCHO retrieval settings have been optimized and harmonized at all the stations, ensuring a consistent validation among the sites. In this validation work, we first assess the accuracy of TROPOMI HCHO tropospheric columns, using the median of the relative differences between TROPOMI and FTIR ground-based data (BIAS). We observe that, at all sites, the TROPOMI accuracy is below the upper limit of the pre-launch requirements of 80 %, and below the lower limit of 40 % for 20 of the 25 stations. The provided TROPOMI systematic uncertainties are well in agreement with the observed biases at most of the stations, except for the highest HCHO levels site where it is found to be underestimated. We find that, while the BIAS has no latitudinal dependence, it is dependent on the HCHO concentration levels: an overestimation (+26 ± 5 %) of TROPOMI is observed for very small HCHO levels ( 8.0 × 1015 molec/cm2). This demonstrates the great value of such a harmonized network covering a wide range of concentration levels, the sites with high HCHO concentrations being crucial for the determination of the satellite bias at the regions of emissions, and the clean sites allowing a small TROPOMI offset to be determined. The wide range of sampled HCHO levels within the network allows the robust determination of the significant constant and proportional TROPOMI HCHO biases (TROPOMI=+ 1.10 (± 0.05) × 1015+ 0.64 (± 0.03) × FTIR, in molec/cm2). Second, the precision of TROPOMI HCHO data is estimated by the median absolute deviation (MAD) of the relative differences between TROPOMI and FTIR ground-based data. The clean sites are especially useful to minimize a possible additional collocation error. The precision requirement of 1.2 × 1016 molec/cm2 for a single pixel is reached at most of the clean sites, where it is found that the TROPOMI precision can even be twice better (0.5–0.8 × 1015 molec/cm2 for a single pixel). However, we find that the provided TROPOMI random uncertainties may be underestimated by a factor of 1.6 (for clean sites) to 2.3 (for high HCHO levels). The correlation is very good between TROPOMI and FTIR data (R = 0.88 for 3 hours-mean coincidences; R = 0.91 for monthly means coincidences). Using about 17 months of data (from May 2018 to September 2019), we show that the TROPOMI seasonal variability is in very good agreement at all of the FTIR sites. The FTIR network demonstrates the very good quality of the TROPOMI HCHO products which is well within the pre-launch requirements for both accuracy and precision. This paper advises for a refinement of the TROPOMI random uncertainty budget and of the TROPOMI quality assurance values for a better filtering of the remaining outliers.

Among the more than 20 ground-based FTIR (Fourier transform infrared) stations currently operating around the globe, only a few have provided formaldehyde (HCHO) total column time series until now. Although several independent studies have shown that the FTIR measurements can provide formaldehyde total columns with good precision, the spatial coverage has not been optimal for providing good diagnostics for satellite or model validation. Furthermore, these past studies used different retrieval settings, and biases as large as 50 % can be observed in the HCHO total columns depending on these retrieval choices, which is also a weakness for validation studies combining data from different ground-based stations.For the present work, the HCHO retrieval settings have been optimized based on experience gained from past studies and have been applied consistently at the 21 participating stations. Most of them are either part of the Network for the Detection of Atmospheric Composition Change (NDACC) or under consideration for membership. We provide the harmonized settings and a characterization of the HCHO FTIR products. Depending on the station, the total systematic and random uncertainties of an individual HCHO total column measurement lie between 12 % and 27 % and between 1 and 11×1014 molec cm−2, respectively. The median values among all stations are 13 % and 2.9×1014 molec cm−2 for the total systematic and random uncertainties.This unprecedented harmonized formaldehyde data set from 21 ground-based FTIR stations is presented and its comparison with a global chemistry transport model shows consistency in absolute values as well as in seasonal cycles. The network covers very different concentration levels of formaldehyde, from very clean levels at the limit of detection (few 1013 molec cm−2) to highly polluted levels (7×1016 molec cm−2). Because the measurements can be made at any time during daylight, the diurnal cycle can be observed and is found to be significant at many stations. These HCHO time series, some of them starting in the 1990s, are crucial for past and present satellite validation and will be extended in the coming years for the next generation of satellite missions.

Multiple tropospheric gases are analyzed in ten years of observations (2010–2019) using a high-resolution ground-based solar absorption Fourier Transform InfraRed (FTIR) instrument in the Colorado Northern Front Range (CNFR). The first year of measurements in 2010 coincides with the start of the remarkable increase of oil and natural (O&NG) extraction in the region. We show seasonal variations and trends of atmospheric gases related to O&NG (C2H6), cattle feedlot activities (NH3), urban emissions (CO, C2H2), biomass burning (HCN), and volatile organic compounds related to photochemistry and ozone production (H2CO, HCOOH). The long-term time series of C2H6 shows clear episodic peak-enhancements related to local O&NG emissions that contribute to a positive trend of 0.9 ± 0.3% ⋅yr−1. NH3 also shows episodic enhancements and has the greatest rate of change for the gases studied here (2.7 ± 0.7% ⋅yr−1). Simulations of all gases are presented using the Community Atmosphere Model with chemistry (CAM-chem) within the Community Earth System Model (CESM) framework. Modeled gases are compared to the observations using different combinations of global emissions in order to determine the best combination for the CNFR. For most gases, using best emissions, the annual rate of change obtained with CAM-chem agrees with the FTIR observations, except for NH3, which is underestimated by a factor of 6. Nevertheless, simulations of NH3 show that the positive trend in NH3 is due to a decrease in its removal via reaction with H2SO4 from a reduction in coal power plant emissions. The seasonal variations of all gases are generally well represented in the model, although magnitudes are often underestimated. The anthropogenic emissions of CO, C2H2, and C2H6 are underestimated by about 20%, 40%, and 65%, respectively, independent of emission inventories. While NH3 summer values are underestimated significantly, other months show low relative mean difference between FTIR observations and CAM-chem simulations. Excellent agreement is found for H2CO, but for HCOOH a factor of 2–3 is needed in the simulations to match observations, pointing to a significant missing source. HCN, a tracer for biomass burning emissions, is well reproduced by the NCAR Fire Inventory (FINN). Furthermore, we show here a simple approach to identify local enhancements of gases related to nearby O&NG and concentrated animal feeding operations. These enhancements above ambient levels are used to estimate emission ratios (ER) of C2H6, H2CO, and HCOOH relative to CO from O&NG air masses. A median ER (and standard deviation) of 0.48 ± 0.41, 0.26 ± 0.15, and 0.13 ± 0.09 [ppb/ppb] are estimated for C2H6, H2CO, and HCOOH, respectively and are representative of the ten years of observations. ER can be used to estimate emission factors (EF), although CO emissions from O&NG need to be well-known. To complement the FTIR observations, we show results derived with airborne observations during The Front Range Air Pollution and Photochemical Experiment (FRAPPE) in 2014. Even though FTIR and FRAPPE observations can not be compared easily they both yield similar median ER. Finally, plumes of fires originated in the western United States in August 2015 were identified and EF are estimated.

Formic (HCOOH) and acetic acids (CH3COOH) are the most abundant carboxylic acids in the Earth's atmosphere and key compounds to aqueous-phase chemistry. Here we present the first distributions of CH3COOH retrieved from the 2007–2018 satellite observations of the nadir-looking infrared atmospheric sounding interferometer (IASI), using a neural network-based retrieval approach. A joint analysis with the IASI HCOOH product reveals that the two species exhibit similar distributions, seasonality, and atmospheric burden, pointing to major common sources. We show that their abundance is highly correlated to isoprene and monoterpenes emissions, as well as to biomass burning. Over Africa, evidence is provided that residual smoldering combustion might be a major driver of the HCOOH and CH3COOH seasonality. Earlier seasonal enhancement of HCOOH at Northern Hemisphere middle and high latitudes and late seasonal secondary peaks of CH3COOH in the tropics suggest that sources and production pathways specific to each species are also at play., SCOPUS: ar.j, info:eu-repo/semantics/published

TROPOMI (the TROPOspheric Monitoring Instrument), on board the Sentinel-5 Precursor (S5P) satellite, has been monitoring the Earth's atmosphere since October 2017 with an unprecedented horizontal resolution (initially 7 km2×3.5 km2, upgraded to 5.5 km2×3.5 km2 in August 2019). Monitoring air quality is one of the main objectives of TROPOMI; it obtains measurements of important pollutants such as nitrogen dioxide, carbon monoxide, and formaldehyde (HCHO). In this paper we assess the quality of the latest HCHO TROPOMI products versions 1.1.(5-7), using ground-based solar-absorption FTIR (Fourier-transform infrared) measurements of HCHO from 25 stations around the world, including high-, mid-, and low-latitude sites. Most of these stations are part of the Network for the Detection of Atmospheric Composition Change (NDACC), and they provide a wide range of observation conditions, from very clean remote sites to those with high HCHO levels from anthropogenic or biogenic emissions. The ground-based HCHO retrieval settings have been optimized and harmonized at all the stations, ensuring a consistent validation among the sites. In this validation work, we first assess the accuracy of TROPOMI HCHO tropospheric columns using the median of the relative differences between TROPOMI and FTIR ground-based data (BIAS). The pre-launch accuracy requirements of TROPOMI HCHO are 40 %–80 %. We observe that these requirements are well reached, with the BIAS found below 80 % at all the sites and below 40 % at 20 of the 25 sites. The provided TROPOMI systematic uncertainties are well in agreement with the observed biases at most of the stations except for the highest-HCHO-level site, where it is found to be underestimated. We find that while the BIAS has no latitudinal dependence, it is dependent on the HCHO concentration levels: an overestimation (+26±5 %) of TROPOMI is observed for very low HCHO levels (<2.5×1015 molec. cm−2), while an underestimation (-30.8%±1.4 %) is found for high HCHO levels (>8.0×1015 molec. cm−2). This demonstrates the great value of such a harmonized network covering a wide range of concentration levels, the sites with high HCHO concentrations being crucial for the determination of the satellite bias in the regions of emissions and the clean sites allowing a small TROPOMI offset to be determined. The wide range of sampled HCHO levels within the network allows the robust determination of the significant constant and proportional TROPOMI HCHO biases (TROPOMI =+1.10±0.05 ×1015+0.64±0.03 × FTIR; in molecules per square centimetre). Second, the precision of TROPOMI HCHO data is estimated by the median absolute deviation (MAD) of the relative differences between TROPOMI and FTIR ground-based data. The clean sites are especially useful for minimizing a possible additional collocation error. The precision requirement of 1.2×1016 molec. cm−2 for a single pixel is reached at most of the clean sites, where it is found that the TROPOMI precision can even be 2 times better (0.5–0.8×1015 molec. cm−2 for a single pixel). However, we find that the provided TROPOMI random uncertainties may be underestimated by a factor of 1.6 (for clean sites) to 2.3 (for high HCHO levels). The correlation is very good between TROPOMI and FTIR data (R=0.88 for 3 h mean coincidences; R=0.91 for monthly means coincidences). Using about 17 months of data (from May 2018 to September 2019), we show that the TROPOMI seasonal variability is in very good agreement at all of the FTIR sites. The FTIR network demonstrates the very good quality of the TROPOMI HCHO products, which is well within the pre-launch requirements for both accuracy and precision. This paper makes suggestions for the refinement of the TROPOMI random uncertainty budget and TROPOMI quality assurance values for a better filtering of the remaining outliers.

We developed a new nitrogen oxide (NOx) and carbon monoxide (CO) emission inventory for the Los Angeles-South Coast Air Basin (SoCAB) expanding the Fuel-based Inventory for motor-Vehicle Emissions and applied it in regional chemical transport modeling focused on the California Nexus of Air Quality and Climate Change (CalNex) 2010 field campaign. The weekday NOx emission over the SoCAB in 2010 is 620 t d−1, while the weekend emission is 410 t d−1. The NOx emission decrease on weekends is caused by reduced diesel truck activities. Weekday and weekend CO emissions over this region are similar: 2340 and 2180 t d−1, respectively. Previous studies reported large discrepancies between the airborne observations of NOx and CO mixing ratios and the model simulations for CalNex based on the available bottom-up emission inventories. Utilizing the newly developed emission inventory in this study, the simulated NOx and CO mixing ratios agree with the observations from the airborne and the ground-based in situ and remote sensing instruments during the field study. The simulations also reproduce the weekly cycles of these chemical species. Both the observations and the model simulations indicate that decreased NOx on weekends leads to enhanced photochemistry and increase of O3 and Ox (=O3 + NO2) in the basin. The emission inventory developed in this study can be extended to different years and other urban regions in the U.S. to study the long-term trends in O3 and its precursors with regional chemical transport models.

From 17–22 August 2017 simultaneous enhancements of ammonia (NH3), carbon monoxide (CO), hydrogen cyanide (HCN), and ethane (C2H6) were detected from ground-based solar absorption Fourier transform infrared (FTIR) spectroscopic measurements at two high-Arctic sites: Eureka (80.05°N, 86.42°W) Nunavut, Canada, and Thule (76.53°N, 68.74°W), Greenland. These enhancements were attributed to wildfires in British Columbia and the Northwest Territories of Canada using FLEXPART back-trajectories and fire locations from Moderate Resolution Imaging Spectroradiometer (MODIS) and found to be the greatest observed enhancements in more than a decade of measurements at Eureka (2006–2017) and Thule (1999–2017). Observations of gas-phase NH3 from these wildfires illustrate that boreal wildfires may be a considerable episodic source of NH3 in the summertime high Arctic. Comparisons of GEOS-Chem model simulations using the Global Fire Assimilation System (GFASv1.2) biomass burning emissions to FTIR measurements and Infrared Atmospheric Sounding Interferometer (IASI) measurements showed that the transport of wildfire emissions to the Arctic was underestimated in GEOS-Chem. However, GEOS-Chem simulations showed that these wildfires contributed to surface layer NH3 and NH4 + enhancements of 0.01–0.11 ppbv and 0.05–1.07 ppbv, respectively, over the Canadian Archipelago from 15–23 August 2017., SCOPUS: ar.j, info:eu-repo/semantics/published

We present an innovative instrument telescope and describe a retrieval method to probe three-dimensional (3-D) distributions of atmospheric trace gases that are relevant to air pollution and tropospheric chemistry. The University of Colorado (CU) two-dimensional (2-D) multi-axis differential optical absorption spectroscopy (CU 2-D-MAX-DOAS) instrument measures nitrogen dioxide (NO2), formaldehyde (HCHO), glyoxal (CHOCHO), oxygen dimer (O2–O2, or O4), and water vapor (H2O); nitrous acid (HONO), bromine monoxide (BrO), and iodine monoxide (IO) are among other gases that can in principle be measured. Information about aerosols is derived through coupling with a radiative transfer model (RTM). The 2-D telescope has three modes of operation: mode 1 measures solar scattered photons from any pair of elevation angle (−20° < EA < +90° or zenith; zero is to the horizon) and azimuth angle (−180° < AA < +180°; zero being north); mode 2 measures any set of azimuth angles (AAs) at constant elevation angle (EA) (almucantar scans); and mode 3 tracks the direct solar beam via a separate view port. Vertical profiles of trace gases are measured and used to estimate mixing layer height (MLH). Horizontal distributions are then derived using MLH and parameterization of RTM (Sinreich et al., 2013). NO2 is evaluated at different wavelengths (350, 450, and 560 nm), exploiting the fact that the effective path length varies systematically with wavelength. The area probed is constrained by O4 observations at nearby wavelengths and has a diurnal mean effective radius of 7.0 to 25 km around the instrument location; i.e., up to 1960 km2 can be sampled with high time resolution. The instrument was deployed as part of the Multi-Axis DOAS Comparison campaign for Aerosols and Trace gases (MAD-CAT) in Mainz, Germany, from 7 June to 6 July 2013. We present first measurements (modes 1 and 2 only) and describe a four-step retrieval to derive (a) boundary layer vertical profiles and MLH of NO2; (b) near-surface horizontal distributions of NO2; (c) range-resolved NO2 horizontal distribution measurements using an "onion-peeling" approach; and (d) the ratios HCHO to NO2 (RFN), CHOCHO to NO2 (RGN), and CHOCHO to HCHO (RGF) at 14 pre-set azimuth angles distributed over a 360° view. Three-dimensional distribution measurements with 2-D-MAX-DOAS provide an innovative, regional perspective of trace gases as well as their spatial and temporal concentration gradients, and they maximize information to compare near-surface observations with atmospheric models and satellites.

Tropospheric chemistry of halogens and organic carbon over tropical oceans modifies ozone and atmospheric aerosols, yet atmospheric models remain largely untested for lack of vertically resolved measurements of bromine monoxide (BrO), iodine monoxide (IO) and small oxygenated hydrocarbons like glyoxal (CHOCHO) in the tropical troposphere. BrO, IO, glyoxal, nitrogen dioxide (NO2), water vapor (H2O) and O2–O2 collision complexes (O4) were measured by the University of Colorado Airborne Multi-AXis Differential Optical Absorption Spectroscopy (CU AMAX-DOAS) instrument, aerosol extinction by high spectral resolution lidar (HSRL), in situ aerosol size distributions by an ultra high sensitivity aerosol spectrometer (UHSAS) and in situ H2O by vertical-cavity surface-emitting laser (VCSEL) hygrometer. Data are presented from two research flights (RF12, RF17) aboard the National Science Foundation/National Center for Atmospheric Research Gulfstream V aircraft over the tropical Eastern Pacific Ocean (tEPO) as part of the "Tropical Ocean tRoposphere Exchange of Reactive halogens and Oxygenated hydrocarbons" (TORERO) project (January/February 2012). We assess the accuracy of O4 slant column density (SCD) measurements in the presence and absence of aerosols. Our O4-inferred aerosol extinction profiles at 477 nm agree within 6% with HSRL in the boundary layer and closely resemble the renormalized profile shape of Mie calculations constrained by UHSAS at low (sub-Rayleigh) aerosol extinction in the free troposphere. CU AMAX-DOAS provides a flexible choice of geometry, which we exploit to minimize the SCD in the reference spectrum (SCDREF, maximize signal-to-noise ratio) and to test the robustness of BrO, IO and glyoxal differential SCDs. The RF12 case study was conducted in pristine marine and free tropospheric air. The RF17 case study was conducted above the NOAA RV Ka'imimoana (TORERO cruise, KA-12-01) and provides independent validation data from ship-based in situ cavity-enhanced DOAS and MAX-DOAS. Inside the marine boundary layer (MBL) no BrO was detected (smaller than 0.5 pptv), and 0.2–0.55 pptv IO and 32–36 pptv glyoxal were observed. The near-surface concentrations agree within 30% (IO) and 10% (glyoxal) between ship and aircraft. The BrO concentration strongly increased with altitude to 3.0 pptv at 14.5 km (RF12, 9.1 to 8.6° N; 101.2 to 97.4° W). At 14.5 km, 5–10 pptv NO2 agree with model predictions and demonstrate good control over separating tropospheric from stratospheric absorbers (NO2 and BrO). Our profile retrievals have 12–20 degrees of freedom (DoF) and up to 500 m vertical resolution. The tropospheric BrO vertical column density (VCD) was 1.5 × 1013 molec cm−2 (RF12) and at least 0.5 × 1013 molec cm−2 (RF17, 0–10 km, lower limit). Tropospheric IO VCDs correspond to 2.1 × 1012 molec cm−2 (RF12) and 2.5 × 1012 molec cm−2 (RF17) and glyoxal VCDs of 2.6 × 1014 molec cm−2 (RF12) and 2.7 × 1014 molec cm−2 (RF17). Surprisingly, essentially all BrO as well as the dominant IO and glyoxal VCD fraction was located above 2 km (IO: 58 ± 5%, 0.1–0.2 pptv; glyoxal: 52 ± 5%, 3–20 pptv). To our knowledge there are no previous vertically resolved measurements of BrO and glyoxal from aircraft in the tropical free troposphere. The atmospheric implications are briefly discussed. Future studies are necessary to better understand the sources and impacts of free tropospheric halogens and oxygenated hydrocarbons on tropospheric ozone, aerosols, mercury oxidation and the oxidation capacity of the atmosphere.

The collision-induced O2 complex, O2O2, is a very important trace gas for understanding remote sensing measurements of aerosols, cloud properties and atmospheric trace gases. Many ground-based multi-axis differential optical absorption spectroscopy (MAX-DOAS) measurements of the O2O2 optical depth require correction factors of 0.75 ± 0.1 to reproduce radiative transfer modeling (RTM) results for a nearly pure Rayleigh atmosphere. One of the potential causes of this discrepancy is uncertainty in laboratory-measured O2O2 absorption cross section temperature and pressure dependencies due to difficulties in replicating atmospheric conditions in the laboratory environment. This paper presents ground-based direct-sun (DS) and airborne multi-axis (AMAX) DOAS measurements of O2O2 absorption optical depths under actual atmospheric conditions in two wavelength regions (335–390 and 435–490 nm). DS irradiance measurements were made by the Washington State University research-grade Multi-Function Differential Spectroscopy Instrument instrument from 2007 to 2014 at seven sites with significant pressure (778 to 1013 hPa) and O2O2 profile-weighted temperature (247 to 275 K) differences. Aircraft MAX-DOAS measurements were conducted by the University of Colorado (CU) AMAX-DOAS instrument on 29 January 2012 over the Southern Hemispheric subtropical Pacific Ocean. Scattered solar radiance spectra were collected at altitudes between 9 and 13.2 km, with O2O2 profile-weighted temperatures of 231 to 244 K and nearly pure Rayleigh scattering conditions. Due to the well-defined DS air-mass factors during ground-based measurements and extensively characterized atmospheric conditions during the aircraft AMAX-DOAS measurements, O2O2 "pseudo" absorption cross sections, σ, are derived from the observed optical depths and estimated O2O2 column densities. Vertical O2O2 columns are calculated from the atmospheric sounding temperature, pressure and specific humidity profiles. Based on the ground-based atmospheric DS observations, there is no pressure dependence of the O2O2 σ within the measurement errors (3%). Two data sets are combined to derive the peak σ temperature dependence of the 360 and 477 nm dimer absorption bands from 231 to 275 K. DS and AMAX-derived peak σ ( O2O2) as a function of T can be described by a quadratic function at 360 nm and linear function at 477 nm with about 9% ± 2.5% per 44 K rate. Recent laboratory-measured O2O2 cross sections by Thalman and Volkamer (2013) agree with these "DOAS apparent" peak σ( O2O2) at 233, 253 and 273 K within 3%. Changes in the O2O2 spectral band shape at colder temperatures are observed for the first time in field data. Temperature effects on spectral band shapes can introduce errors in the retrieved O2O2 column abundances if a single room temperature σ( O2O2) is used in the DOAS analysis. Simultaneous fitting of σ( O2O2) at temperatures that bracket the ambient temperature range can reduce such errors. Our results show that laboratory-measured σ( O2O2) (Hermans, 2011, at 296 K and Thalman and Volkamer, 2013) are applicable for observations over a wide range of atmospheric conditions. Column densities derived using Hermans (2011) σ at 296 K require very small correction factors (0.94 ± 0.02 at 231 K and 0.99 ± 0.02 at 275 K) to reproduce theoretically calculated slant column densities for DS and AMAX-DOAS measurements. Simultaneous fitting of σ( O2O2) at 203 and 293 K further improved the results at UV and visible wavelengths for AMAX-DOAS.

In order to promote the development of the passive DOAS technique the Multi Axis DOAS – Comparison campaign for Aerosols and Trace gases (MAD-CAT) was held at the Max Planck Institute for Chemistry in Mainz, Germany from June to October 2013. Here, we systematically compare the differential slant column densities (dSCDs) of nitrous acid (HONO) derived from measurements of seven different instruments. We also compare the tropospheric difference of SCDs (delta SCD) of HONO, namely the difference of the SCDs for the non-zenith observations and the zenith observation of the same elevation sequence. Different research groups analysed the spectra from their own instruments using their individual fit software. All the fit errors of HONO dSCDs from the instruments with cooled large-size detectors are mostly in the range of 0.1 to 0.3 × 1015 molecules cm−2 for an integration time of 1 min. The fit error for the mini MAX-DOAS is around 0.7 × 1015 molecules cm−2. Although the HONO delta SCDs are normally smaller than 6 × 1015 molecules cm−2, consistent time series of HONO delta SCDs are retrieved from the measurements of different instruments. Both fits with a sequential Fraunhofer reference spectrum (FRS) and a daily noon FRS lead to similar consistency. Apart from the mini-MAX-DOAS, the systematic absolute differences of HONO delta SCDs between the instruments are smaller than 0.63 × 1015 molecules cm−2. The correlation coefficients are higher than 0.7 and the slopes of linear regressions deviate from unity by less than 16% for the elevation angle of 1°. The correlations decrease with an increase of elevation angle. All the participants also analysed synthetic spectra using the same baseline DOAS settings to evaluate the systematic errors of HONO results from their respective fit programs. In general the errors are smaller than 0.3 × 1015 molecules cm−2, which is about half of the systematic difference between the real measurements. The differences of HONO delta SCDs between retrieved in the selected three spectral ranges 335–361 nm, 335–373 nm and 335–390 nm are considerable (up to 0.57 × 1015 molecules cm−2) for both real measurements and synthetic spectra. We performed sensitivity studies to quantify the dominant systematic error sources and to find a recommended DOAS setting in the three spectral ranges. The results show that water vapour absorption, temperature and wavelength dependence of O4 absorption, temperature dependence of Ring spectrum, and polynomial and intensity offset correction all together dominate the systematic errors. We recommend a fit range of 335–373 nm for HONO retrievals. In such fit range the total systematic uncertainty from different sources is about 0.87 × 1015 molecules cm−2, much smaller than those in the other two ranges. Meanwhile the systematic bias of the fitted from the simulated real HONO delta SCDs is also smallest in 335–373 nm (about 0.02 × 1015 molecules cm−2). The typical random uncertainty is estimated to be about 0.16 × 1015 molecules cm−2, which is only 25 % of the total systematic uncertainty for most of the instruments in the MAD-CAT campaign. In summary most of the MAX-DOAS instruments can well observe the signals of atmospheric HONO absorption in case of HONO delta SCDs higher than 0.2 × 1015 molecules cm−2. However, systematic uncertainties limit the reliability of the results.

Cell penetrating peptides (CPP) and cationic antibacterial peptides (CAP) have similar physicochemical properties and yet it is not understood how such similar peptides display different activities. To address this question, we used Iztli peptide 1 (IP-1) because it has both CPP and CAP activities. Combining experimental and computational modeling of the internalization of IP-1, we show it is not internalized by receptor-mediated endocytosis, yet it permeates into many different cell types, including fungi and human cells. We also show that IP-1 makes pores in the presence of high electrical potential at the membrane, such as those found in bacteria and mitochondria. These results provide the basis to understand the functional redundancy of CPPs and CAPs.

The University of Colorado Airborne Multi-Axis Differential Optical Absorption Spectroscopy (CU AMAX-DOAS) instrument uses solar stray light to detect and quantify multiple trace gases, including nitrogen dioxide (NO2), glyoxal (CHOCHO), formaldehyde (HCHO), water vapor (H2O), nitrous acid (HONO), iodine monoxide (IO), bromine monoxide (BrO), and oxygen dimers (O4) at multiple wavelengths (absorption bands at 360, 477, 577, 632 nm) simultaneously in the open atmosphere. The instrument is unique as it (1) features a motion compensation system that decouples the telescope field of view from aircraft movements in real time ( The instrument is described, and data from flights over California during the CalNex (California Research at the Nexus of Air Quality and Climate Change) and CARES (Carbonaceous Aerosols and Radiative Effects Study) air quality field campaigns is presented. Horizontal distributions of NO2 VCD (below the aircraft) maps are sampled with typically 1 km resolution, and show good agreement with two ground-based MAX-DOAS instruments (slope = 0.95 ± 0.09, R2 = 0.86). As a case study vertical profiles of NO2, CHOCHO, HCHO, and H2O concentrations and aerosol extinction coefficients, ε, at 477 nm calculated from O4 measurements from a low approach at Brackett airfield inside the South Coast Air Basin (SCAB) are presented. These profiles contain ~12 degrees of freedom (DOF) over a 3.5 km altitude range, an independent information approximately every 250 m. The boundary layer NO2 concentration, and the integral aerosol extinction over height (aerosol optical depth, AOD) agrees well with nearby ground-based in situ NO2 measurement, and AERONET station. The detection limits of NO2, CHOCHO, HCHO, H2O442, &varepsilon;360, &varepsilon;477 for 30 s integration time spectra recorded forward of the plane are 5 ppt, 3 ppt, 100 ppt, 42 ppm, 0.004 km−1, 0.002 km−1 in the free troposphere (FT), and 30 ppt, 16 ppt, 540 ppt, 252 ppm, 0.012 km−1, 0.006 km−1 inside the boundary layer (BL), respectively. Mobile column observations of trace gases and aerosols are complimentary to in situ observations, and help bridge the spatial scales that are probed by satellites and ground-based observations, and predicted by atmospheric models.

Continuous carbon monoxide (CO) total column densities above the Universidad Nacional Autónoma de México (UNAM) campus in Mexico City have been derived from solar absorption infrared spectroscopic measurements since October 2007. Its diurnal evolution is used in the present study in conjunction with other ground-based and satellite data to develop a top-down emission estimate of the annual CO emission of the Mexico City Metropolitan Area (MCMA). The growth-rate of the total column around noon under low ventilation conditions is calculated and allows us to derive the average surface emission-flux at UNAM, while similar measurements taken at the edge of the MCMA in Tecámac provide information on background CO levels in the Mexico basin. Based on 3 yr of measurements, CO column measurements from the Infrared Atmospheric Sounding Interferometer (IASI) satellite instrument are used to reconstruct the spatial distribution of this anthropogenic pollutant over the MCMA. The agreement between the measured columns of the satellite and ground-based measurements is excellent, particularly when a comparison strategy based on time-displaced air masses is used. The annual emission of the Mexico Megacity is estimated to be (2.15 ± 0.5) Tg yr-1 for the year 2008, while the official inventory for that year reported 1.6 Tg yr -1. The difference is slightly higher than the conservative uncertainty estimated in this work suggesting that the emission might be underestimated by the conventional bottom-up method. A larger discrepancy is found in the spatial distribution of the emissions, when comparing the emission flux over UNAM (derived from the ground-based measurement) with that of the inventory integrated over a representative area. The methodology presented here represents a new and useful strategy to evaluate the contribution of megacities to the global anthropogenic gas emissions. Additionally, three different strategies to compare ground and space-based measurements above an inhomogeneous and strongly contaminated area like Mexico City are presented and discussed. © Author(s) 2013., SCOPUS: ar.j, info:eu-repo/semantics/published

Tropospheric chemistry of halogens and organic carbon over tropical oceans modifies ozone and atmospheric aerosols, yet atmospheric models remain largely untested for lack of vertically resolved measurements of bromine monoxide (BrO), iodine monoxide (IO), and small oxygenated hydrocarbons like glyoxal (CHOCHO) in the tropical troposphere. BrO, IO, glyoxal, nitrogen dioxide (NO2), water vapor (H2O) and O2-O2 collision complexes (O4) were measured by the CU Airborne Multi AXis Differential Optical Absorption Spectroscopy (CU AMAX-DOAS) instrument, in situ aerosol size distributions by an Ultra High Sensitivity Aerosol Spectrometer (UHSAS), and in situ H2O by Vertical-Cavity Surface-Emitting Laser hygrometer (VCSEL). Data are presented from two research flights (RF12, RF17) aboard the NSF/NCAR GV aircraft over the tropical Eastern Pacific Ocean (tEPO) as part of the "Tropical Ocean tRoposphere Exchange of Reactive halogens and Oxygenated hydrocarbons" (TORERO) project. We assess the accuracy of O4 slant column density (SCD) measurements in the presence and absence of aerosols, and find O4-inferred aerosol extinction profiles at 477 nm agree within 5% with Mie calculations of extinction profiles constrained by UHSAS. CU AMAX-DOAS provides a flexible choice of geometry which we exploit to minimize the SCD in the reference spectrum (SCDREF, maximize signal-to-noise), and to test the robustness of BrO, IO, and glyoxal differential SCDs. The RF12 case study was conducted in pristine marine and free tropospheric air. The RF17 case study was conducted above the NOAA RV Ka'imimoana (TORERO cruise, KA-12-01), and provides independent validation data from ship-based in situ Cavity Enhanced- and MAX-DOAS. Inside the marine boundary layer (MBL) no BrO was detected (smaller than 0.5 pptv), and 0.2–0.55 pptv IO and 32–36 pptv glyoxal were observed. The near surface concentrations agree within 20% (IO) and 10% (glyoxal) between ship and aircraft. The BrO concentration strongly increased with altitude to 3.0 pptv at 14.5 km (RF12, 9.1 to 8.6° N; 101.2 to 97.4° W). At 14.5 km 5–10 pptv NO2 agree with model predictions, and demonstrate good control over separating tropospheric from stratospheric absorbers (NO2 and BrO). Our profile retrievals have 12–20 degrees of freedom (DoF), and up to 500 m vertical resolution. The tropospheric BrO VCD was 1.5 × 1013 molec cm−2 (RF12), and at least 0.5 × 1013 molec cm−2 (RF17, 0–10 km, lower limit). Tropospheric IO VCDs correspond to 2.1 × 1012 molec cm−2 (RF12) and 2.5 × 1012 molec cm−2 (RF17), and glyoxal VCDs of 2.6 × 1014 molec cm−2 (RF12) and 2.7 × 1014 molec cm−2 (RF17). Surprisingly, essentially all BrO, and the dominant IO and glyoxal VCD fraction was located above 2 km (IO: 58 ± 5%, 0.1–0.2 pptv; glyoxal: 52 ± 5%, 3–20 pptv). To our knowledge there are no previous vertically resolved measurements of BrO and glyoxal from aircraft in the tropical free troposphere.

The collision induced O2 complex, O2O2, is a very important trace gas in remote sensing measurements of aerosol and cloud properties. Some ground based MAX-DOAS measurements of O2O2 slant column density require correction factors of 0.75 ± 0.1 to reproduce radiative transfer modeling (RTM) results for a near pure Rayleigh atmosphere. One of the potential causes of this discrepancy is believed to be uncertainty in laboratory measured O2O2 absorption cross section temperature and pressure dependence, due to difficulties in replicating atmospheric conditions in the laboratory environment. This paper presents direct-sun (DS) and airborne multi-axis (AMAX) DOAS measurements of O2O2 absorption optical depths under actual Earth atmospheric conditions in two wavelength regions (335–390 nm and 435–490 nm). DS irradiance measurements were made by the research grade MFDOAS instrument from 2007–2014 at seven sites with significant pressure (778–1013 hPa) and O2O2 profile weighted temperature (247–275 K) differences. Aircraft MAX-DOAS measurements were conducted by the University of Colorado AMAX-DOAS instrument on 29 January 2012 over the Southern Hemisphere subtropical Pacific Ocean. Scattered solar radiance spectra were collected at altitudes between 9 and 13.2 km, with O2O2 profile weighted temperatures of 231–244 K, and near pure Rayleigh scattering conditions. Due to the well defined DS air mass factors and extensively characterized atmospheric conditions during the AMAX-DOAS measurements, O2O2"pseudo" absorption cross sections, σ, are derived from the observed optical depths and estimated O2O2column densities. Vertical O2O2 columns are calculated from the atmospheric sounding temperature, pressure and specific humidity profiles. Based on the atmospheric DS observations, there is no pressure dependence of the O2O2 σ, within the measurement errors (3%). The two data sets are combined to derive peak σ temperature dependence of 360 and 477 nm absorption bands from 231–275 K. DS and AMAX derived peak σ(O2O2) as a function of T can be described by a quadratic function at 360 nm and linear at 477 nm with about 9 ± 2.5% per 44 K rate. Recent laboratory measured O2O2 cross sections by Thalman and Volkamer (2013) agree with these "DOAS apparent" peak σ(O2O2) at 233 K, 253 K and 273 K within 3%. Changes in the O2O2 spectral band-shape at colder temperatures are for the first time also observed in field data. Temperature effects on spectral band shapes can introduce errors in the retrieved O2O2 column abundances if a single room temperature σ(O2O2) is used in the DOAS analysis. Simultaneous fitting of σ(O2O2) at temperatures that bracket the ambient temperature range can reduce such errors. Our results suggest that laboratory measured σ(O2O2) (Hermans et al. (2011) at 296 K and Thalman and Volkamer (2013)) are applicable for observations over a wide range of atmospheric conditions. Column densities derived using Hermans et al. (2011) σ at 296 K require very small correction factors (0.94 ± 0.02 at 231 K and 0.99 ± 0.02 at 275 K) to reproduce theoretically calculated SCDs for DS and AMAX-DOAS measurements. Simultaneous fitting of σ(O2O2) at 203 and 293 K further improved results at UV and visible wavelengths for AMAX-DOAS.

Here we present first eddy covariance (EC) measurements of fluxes of glyoxal, the smallest α-dicarbonyl product of hydrocarbon oxidation, and a precursor for secondary organic aerosol (SOA). The unique physical and chemical properties of glyoxal – i.e., high solubility in water (effective Henry's law constant, KH = 4.2 × 105 M atm−1) and short atmospheric lifetime (~2 h at solar noon) – make it a unique indicator species for organic carbon oxidation in the marine atmosphere. Previous reports of elevated glyoxal over oceans remain unexplained by atmospheric models. Here we describe a Fast Light-Emitting Diode Cavity-Enhanced Differential Optical Absorption Spectroscopy (Fast LED-CE-DOAS) instrument to measure diurnal variations and EC fluxes of glyoxal and inform about its unknown sources. The fast in situ sensor is described, and first results are presented from a cruise deployment over the eastern tropical Pacific Ocean (20° N to 10° S; 133 to 85° W) as part of the Tropical Ocean tRoposphere Exchange of Reactive halogens and Oxygenated VOCs (TORERO) field experiment (January to March 2012). The Fast LED-CE-DOAS is a multispectral sensor that selectively and simultaneously measures glyoxal (CHOCHO), nitrogen dioxide (NO2), oxygen dimers (O4), and water vapor (H2O) with ~2 Hz time resolution (Nyquist frequency ~1 Hz) and a precision of ~40 pptv Hz−0.5 for glyoxal. The instrument is demonstrated to be a "white-noise" sensor suitable for EC flux measurements. Fluxes of glyoxal are calculated, along with fluxes of NO2, H2O, and O4, which are used to aid the interpretation of the glyoxal fluxes. Further, highly sensitive and inherently calibrated glyoxal measurements are obtained from temporal averaging of data (e.g., detection limit smaller than 2.5 pptv in an hour). The campaign average mixing ratio in the Southern Hemisphere (SH) is found to be 43 ± 9 pptv glyoxal, which is higher than the Northern Hemisphere (NH) average of 32 ± 6 pptv (error reflects variability over multiple days). The diurnal variation of glyoxal in the marine boundary layer (MBL) is measured for the first time, and mixing ratios vary by ~8 pptv (NH) and ~12 pptv (SH) over the course of 24 h. Consistently, maxima are observed at sunrise (NH: 35 ± 5 pptv; SH: 47 ± 7 pptv), and minima at dusk (NH: 27 ± 5 pptv; SH: 35 ± 8 pptv). In both hemispheres, the daytime flux was directed from the atmosphere into the ocean, indicating that the ocean is a net sink for glyoxal during the day. After sunset the ocean was a source for glyoxal to the atmosphere (positive flux) in the SH; this primary ocean source was operative throughout the night. In the NH, the nighttime flux was positive only shortly after sunset and negative during most of the night. Positive EC fluxes of soluble glyoxal over oceans indicate the presence of an ocean surface organic microlayer (SML) and locate a glyoxal source within the SML. The origin of most atmospheric glyoxal, and possibly other oxygenated hydrocarbons over tropical oceans, remains unexplained and warrants further investigation.

To evaluate the efficacy and safety of amide derivative of amphotericin B, as scaling product at in vitro experimental assays. Amphotericin B (AmB) has been considered the gold standard drug for treating mycosis, however, it produce nephrotoxicity, hepatotoxicity and hemolytic anemia. For evaluating the antifungal activity of the AmB and DA, we used six strains of Candida. Yeasts were seeded in 96-well plates in SD broth media. Cells were treated with AmB and DA at concentrations of 1, 10, 50, 100, 250 and 500 mM and 0.1 to 1 µM in order to determine the IC50. Safety was evaluate in kidney and liver cells. These cells were treated with AmB and DA at different concentrations 1, 10, 50, 100, 250 and 500 μM and the citotoxicity was evaluated by MTT technique and also identified the type of cell death by immunofluorescence microscopy. The DA was effective on 6 yeast Candida species treated with AmB and DA. IC50 founds were: C. albicans (SC5314) AmB= 0.13 µM vs DA= 0.26 µM; C. albicans (10231) AmB= 0.13 µMvs D...

In the first paper of this series, we will describe a method, called effective group potentials (EGP), aimed at simplifying molecular ab initio calculations for large systems involving bulky ligands as long as these ligands can be supposed to play the role of spectator groups. This method should be applicable to all types of bondings between active and the spectator parts. The different steps used in the definition of the EGP are closely related to those used for atomic effective core potentials (ECP) which are commonly used with great success in ab initio calculations involving heavy atoms.

Thymidylate synthase (TS) is a homodimeric enzyme with two equivalent active sites composed of residues from both subunits. Despite the structural symmetry of the enzyme, certain experimental results are consistent with half-the-sites activity, suggesting negative cooperativity between the active sites. To gain insight into the mechanism behind this phenomenon, we explore segmental motions of rat TS in the absence of ligands, with normal mode analysis as a tool. Using solvent accessible surface area of the active site pocket as a monitor of the degree of opening of the active sites, we classified the first 25 nontrivial normal modes, obtained from the web server of the program ElNemo, according to the behavior of the active sites. We found seven modes that open and close both sites symmetrically and nine that do so in an anticorrelated fashion. We characterized the motions of these modes by visual inspection and through measurement of distances between selected atoms lining the active site pockets. The segments that regulate access to the active site correspond to the loop containing R44, helix K, and a long loop containing residues 103–125, in agreement with a large body of crystallographic studies. These elements can be activated together or in isolation. There are more asymmetric modes than symmetric ones in the set we analyzed, probably accounting for the half-the-sites behavior of the enzyme. Three of the asymmetric modes result in changes at the dimer interface and indicate the endpoints of possible communication pathways between the active sites. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 549–559, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

Ab initio quantum mechanical calculations were used to study the hydrolysis reaction H4P2O7 + H2O in equilibrium with 2H3PO4, as well as some molecular properties of the reactants and products. SCF calculations with several basis sets ranging from minimal to extended with polarization functions were used to look at the basis dependency of the reaction enthalpies and optimized geometries. Although the minimal basis sets yield erratic predictions of the enthalpy, when a more extended basis (3-21G*) was used for the geometry optimization, and the total energies of the reactants and products were computed with this and larger basis sets, we obtained more consistent predictions of the structural properties of the P-O-P bridge and of the heat of the hydrolysis reaction (delta E = -7.39 kcal/mol at the SCF/6-31G** level). A comparison is made with previous estimates performed with smaller basis sets and without taking into account the electron correlation effects, which are calculated in the present work. The inclusion of the zero point energy calculated using the harmonic approximation, and of the electronic correlation energy determined at the MBPT(2) level, raised the computed heat of the reaction to -3.83 kcal/mol, and when an estimate for the thermal energy was added, the value obtained was of -3.38 kcal/mol. In conclusion, we found that the hydrolysis of pyrophosphate should be exothermic in the gas phase. The implications of this result in relation to some recent theories about enzyme catalysis are discussed.

The Lowdin theory for the molecular basis of spontaneous mutations is reviewed. It is concluded that with the evidence now available the general theory remains valid but the treatment of irreversible mutations should be modified. A reading mechanism that enables the Lowdin model for transcription to reproduce experimental observations is proposed. Transcription of a closed DNA molecule is then advanced as an alternative mechanism of RNA synthesis and experiments to test this are suggested.