Survival of newly formed particles in haze conditions

Intense new particle formation events are regularly observed under highly polluted conditions, despite the high loss rates of nucleated clusters. Higher than expected cluster survival probability implies either ineffective scavenging by pre-existing particles or missing growth mechanisms. Here we present experiments performed in the CLOUD chamber at CERN showing particle formation from a mixture of anthropogenic vapours, under condensation sinks typical of haze conditions, up to 0.1 s&minus;1. We find that new particle formation rates substantially decrease at higher concentrations of pre-existing particles, demonstrating experimentally for the first time that molecular clusters are efficiently scavenged by larger sized particles. Additionally, we demonstrate that in the presence of supersaturated gas-phase nitric acid (HNO3) and ammonia (NH3), freshly nucleated particles can grow extremely rapidly, maintaining a high particle number concentration, even in the presence of a high condensation sink. Such high growth rates may explain the high survival probability of freshly formed particles under haze conditions. We identify under what typical urban conditions HNO3 and NH3 can be expected to contribute to particle survival during haze. &nbsp;</p

A DOAS Study on the Oxidation Mechanism of Aromatic Hydrocarbons under Simulated Atmospheric Conditions

Das Ziel dieser Arbeit war es das Verständnis der OH-Radikal initiierten Oxidation aromatischer Kohlenwasserstoffe (Benzol, Toluol, p-Xylol (BTX) und 1,3,5-Trimethylbenzol (TMB)) zu verbessern. Diese Mechanismen gelten als Hauptunsicherheitsfaktoren in Chemie-Modellen zur Erfassung der Photooxidantienbildung aus Stadtluft. Differentielle Optische Absorptions Spektroskopie (DOAS) wurde in einer systematischen Smog-Kammer Studie am Europäischen Photoreaktor (EUPHORE), CEAM-Institute, Valencia/Spanien angewandt. Das vorhandene DOAS-System wurde hierzu weiterentwickelt. Die Verzweigungsverhältnisse (Yields) der ringerhaltenden Produkte (Phenol von Benzol, Phenole und Aldehyde von p-Xylol und TMB) sowie Glyoxal (von BTX) wurden bestimmt. Der Phenol-Yield aus Benzol (F(PHEN) = 53) wurde zu mehr als dem doppelten des Literaturwertes bestimmt. Weiterhin wurde der Ringspaltungsmechanismus über das Bicycloalkyl-Radikal als einer der Hauptwege in der Oxidation von BTX identifiziert. Es wurde gezeigt, daß die Ergebnisse dieser Arbeit repräsentativ sind für die Atmosphäre. Abweichungen von den atmosphärisch relevanten Reaktionswegen von BTX und TMB wurden in Anwesenheit von hohen NOx-Konzentrationen (einige ppm) beobachtet. Die Resultate dieser Arbeit werden von heute verwendeten Aromat-Mechanismen in Chemie Modellen nur unzureichend beschrieben. Die Ergebnisse zeigen, daß der Beitrag von Aromaten zur Bildung von Photooxidantien (z.B. Ozon) bislang unterschätzt wird

Radicals and aerosols in the troposphere and lower stratosphere

The remote tropical free troposphere (FT) is one of the most relevant atmospheric environments on Earth. About 75\% of the global tropospheric O3 and CH4 loss occurs at tropical latitudes. Tropospheric bromine and iodine catalytically destroy tropospheric O$_{3}$, oxidize atmospheric mercury, and modify oxidative capacity, and aerosols. Oxygenated VOCs (OVOC) modify HO$_{x}$ (= OH + HO$_{2}$), NOx (= NO + NO$_{2}$), tropospheric O$_{3}$, aerosols, and are a sink for BrO$_{x}$ (= Br + BrO). Until recently, atmospheric models were untested for lack of vertically resolved measurements of BrO and IO radicals in the tropical troposphere. BrO and IO are highly reactive trace gases. Even very low concentrations (parts per trillion1 pptv = 10$^{-12}$ volume mixing ratio) can significantly modify the lifetime of climate active gases, and determine (bromine) the rate limiting step of mercury oxidation in air (that is washed out, and subsequently bio-accumulates in fish). Analytical challenges arise when these radicals modify in sampling lines. Sensitive yet robust, portable, and inherently calibrated measurements directly in the open atmosphere have recently been demonstrated by means of limb-measurements of scattered solar photons by the University of Colorado Airborne Multi-AXis DOAS instrument (CU AMAX-DOAS) from research aircraft. The CU AMAX-DOAS instrument is optimized to (1) locate BrO, IO and glyoxal (a short lived OVOC) in the troposphere, (2) decouple stratospheric absorbers, (3) maximize sensitivity at instrument altitude, (4) facilitate altitude control and (5) enable observations over a wide range of solar zenith angles. Further, (6) the filling-in of Fraunhofer lines (Ring-effect) by Raman Scattering offers interesting opportunities for radiative closure studies to assess the effects of aerosols on Climate

Modelling the gas-particle partitioning and water uptake of isoprene-derived secondary organic aerosol at high and low relative humidity

This study presents a characterization of the hygroscopic growth behaviour and effects of different inorganic seed particles on the formation of secondary organic aerosols (SOAs) from the dark ozone-initiated oxidation of isoprene at low NOx conditions. We performed simulations of isoprene oxidation using a gas-phase chemical reaction mechanism based on the Master Chemical Mechanism (MCM) in combination with an equilibrium gas&ndash;particle partitioning model to predict the SOA concentration. The equilibrium model accounts for non-ideal mixing in liquid phases, including liquid&ndash;liquid phase separation (LLPS), and is based on the AIOMFAC (Aerosol Inorganic&ndash;Organic Mixtures Functional groups Activity Coefficients) model for mixture non-ideality and the EVAPORATION (Estimation of VApour Pressure of ORganics, Accounting for Temperature, Intramolecular, and Non-additivity effects) model for pure compound vapour pressures. Measurements from the Cosmics Leaving Outdoor Droplets (CLOUD) chamber experiments, conducted at the European Organization for Nuclear Research (CERN) for isoprene ozonolysis cases, were used to aid in parameterizing the SOA yields at different atmospherically relevant temperatures, relative humidity (RH), and reacted isoprene concentrations. To represent the isoprene-ozonolysis-derived SOA, a selection of organic surrogate species is introduced in the coupled modelling system. The model predicts a single, homogeneously mixed particle phase at all relative humidity levels for SOA formation in the absence of any inorganic seed particles. In the presence of aqueous sulfuric acid or ammonium bisulfate seed particles, the model predicts LLPS to occur below &sim;&thinsp;80&thinsp;% RH, where the particles consist of an inorganic-rich liquid phase and an organic-rich liquid phase; however, this includes significant amounts of bisulfate and water partitioned to the organic-rich phase. The measurements show an enhancement in the SOA amounts at 85&thinsp;% RH, compared to 35&thinsp;% RH, for both the seed-free and seeded cases. The model predictions of RH-dependent SOA yield enhancements at 85&thinsp;% RH vs. 35&thinsp;% RH are 1.80 for a seed-free case, 1.52 for the case with ammonium bisulfate seed, and 1.06 for the case with sulfuric acid seed. Predicted SOA yields are enhanced in the presence of an aqueous inorganic seed, regardless of the seed type (ammonium sulfate, ammonium bisulfate, or sulfuric acid) in comparison with seed-free conditions at the same RH level. We discuss the comparison of model-predicted SOA yields with a selection of other laboratory studies on isoprene SOA formation conducted at different temperatures and for a variety of reacted isoprene concentrations. Those studies were conducted at RH levels at or below 40&thinsp;% with reported SOA mass yields ranging from 0.3&thinsp;% up to 9.0&thinsp;%, indicating considerable variations. A robust feature of our associated gas&ndash;particle partitioning calculations covering the whole RH range is the predicted enhancement of SOA yield at high RH (&gt;&thinsp;80&thinsp;%) compared to low RH (dry) conditions, which is explained by the effect of particle water uptake and its impact on the equilibrium partitioning of all components. &nbsp;</p

Global tropospheric halogen (Cl, Br, I) chemistry and its impact on oxidants

We present an updated mechanism for tropospheric halogen (Cl&thinsp;+&thinsp;Br&thinsp;+&thinsp;I) chemistry in the GEOS-Chem global atmospheric chemical transport model and apply it to investigate halogen radical cycling and implications for tropospheric oxidants. Improved representation of HOBr heterogeneous chemistry and its pH dependence in our simulation leads to less efficient recycling and mobilization of bromine radicals and enables the model to include mechanistic sea salt aerosol debromination without generating excessive BrO. The resulting global mean tropospheric BrO mixing ratio is 0.19&thinsp;ppt (parts per trillion), lower than previous versions of GEOS-Chem. Model BrO shows variable consistency and biases in comparison to surface and aircraft observations in marine air, which are often near or below the detection limit. The model underestimates the daytime measurements of Cl2 and BrCl from the ATom aircraft campaign over the Pacific and Atlantic, which if correct would imply a very large missing primary source of chlorine radicals. Model IO is highest in the marine boundary layer and uniform in the free troposphere, with a global mean tropospheric mixing ratio of 0.08&thinsp;ppt, and shows consistency with surface and aircraft observations. The modeled global mean tropospheric concentration of Cl atoms is 630&thinsp;cm&minus;3, contributing 0.8&thinsp;% of the global oxidation of methane, 14&thinsp;% of ethane, 8&thinsp;% of propane, and 7&thinsp;% of higher alkanes. Halogen chemistry decreases the global tropospheric burden of ozone by 11&thinsp;%, NOx by 6&thinsp;%, and OH by 4&thinsp;%. Most of the ozone decrease is driven by iodine-catalyzed loss. The resulting GEOS-Chem ozone simulation is unbiased in the Southern Hemisphere but too low in the Northern Hemisphere. &nbsp; Full List of Authors: Xuan Wang1,2, Daniel J. Jacob3, William Downs3, Shuting Zhai4, Lei Zhu5, Viral Shah3, Christopher D. Holmes6, Tom&aacute;s Sherwen7,8, Becky Alexander4, Mathew J. Evans7,8, Sebastian D. Eastham9, J. Andrew Neuman10,11, Patrick R. Veres10, Theodore K. Koenig11,12, Rainer Volkamer11,12, L. Gregory Huey13, Thomas J. Bannan14, Carl J. Percival14,a, Ben H. Lee4, and Joel A. Thornton4 1School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China 2City University of Hong Kong Shenzhen Research Institute, Shenzhen, China 3School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA 4Department of Atmospheric Sciences, University of Washington, Seattle, Washington, USA 5School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China 6Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, Florida, USA 7Wolfson Atmospheric Chemistry Laboratories, Department of Chemistry, University of York, York, UK 8National Centre for Atmospheric Science, University of York, York, UK 9Laboratory for Aviation and the Environment, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA 10NOAA Chemical Sciences Laboratory (CSL), Boulder, Colorado, USA 11Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA 12Department of Chemistry, University of Colorado, Boulder, Colorado, USA 13School of Earth and Atmospheric Science, Georgia Institute of Technology, Atlanta, Georgia, USA 14School of Earth, Atmospheric and Environmental Sciences, University of Manchester, Manchester, UK anow at: Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA &nbsp;</p

Inter-comparison of MAX-DOAS measurements of tropospheric HONO slant column densities and vertical profiles during the CINDI-2 campaign

We present the inter-comparison of delta slant column densities (SCDs) and vertical profiles of nitrous acid (HONO) derived from measurements of different multi-axis differential optical absorption spectroscopy (MAX-DOAS) instruments and using different inversion algorithms during the Second Cabauw Inter-comparison campaign for Nitrogen Dioxide measuring Instruments (CINDI-2) in September&nbsp;2016 at Cabauw, the Netherlands (51.97∘&thinsp;N, 4.93∘&thinsp;E). The HONO vertical profiles, vertical column densities (VCDs), and near-surface volume mixing ratios are compared between different MAX-DOAS instruments and profile inversion algorithms for the first time. Systematic and random discrepancies of the HONO results are derived from the comparisons of all data sets against their median values. Systematic discrepancies of HONO delta SCDs are observed in the range of &plusmn;0.3&times;1015&thinsp;molec.&thinsp;cm&minus;2, which is half of the typical random discrepancy of 0.6&times;1015&thinsp;molec.&thinsp;cm&minus;2. For a typical high HONO delta SCD of 2&times;1015&thinsp;molec.&thinsp;cm&minus;2, the relative systematic and random discrepancies are about 15&thinsp;% and 30&thinsp;%, respectively. The inter-comparison of HONO profiles shows that both systematic and random discrepancies of HONO VCDs and near-surface volume mixing ratios (VMRs) are mostly in the range of &sim;&plusmn;0.5&times;1014&thinsp;molec.&thinsp;cm&minus;2 and &sim;&plusmn;0.1&thinsp;ppb (typically &sim;20&thinsp;%). Further we find that the discrepancies of the retrieved HONO profiles are dominated by discrepancies of the HONO delta SCDs. The profile retrievals only contribute to the discrepancies of the HONO profiles by &sim;5&thinsp;%. However, some data sets with substantially larger discrepancies than the typical values indicate that inappropriate implementations of profile inversion algorithms and configurations of radiative transfer models in the profile retrievals can also be an important uncertainty source. In addition, estimations of measurement uncertainties of HONO dSCDs, which can significantly impact profile retrievals using the optimal estimation method, need to consider not only DOAS fit errors, but also atmospheric variability, especially for an instrument with a DOAS fit error lower than &sim;3&times;1014&thinsp;molec.&thinsp;cm&minus;2. The MAX-DOAS results during the CINDI-2 campaign indicate that the peak HONO levels (e.g. near-surface VMRs of &sim;0.4&thinsp;ppb) often appeared in the early morning and below 0.2&thinsp;km. The near-surface VMRs retrieved from the MAX-DOAS observations are compared with those measured using a co-located long-path DOAS instrument. The systematic differences are smaller than 0.15 and 0.07&thinsp;ppb during early morning and around noon, respectively. Since true HONO values at high altitudes are not known in the absence of real measurements, in order to evaluate the abilities of profile inversion algorithms to respond to different HONO profile shapes, we performed sensitivity studies using synthetic HONO delta SCDs simulated by a radiative transfer model with assumed HONO profiles. The tests indicate that the profile inversion algorithms based on the optimal estimation method with proper configurations can reproduce the different HONO profile shapes well. Therefore we conclude that the features of HONO accumulated near the surface derived from MAX-DOAS measurements are expected to represent the ambient HONO profiles well. Full List of Authors: Yang Wang1, Arnoud Apituley2, Alkiviadis Bais3, Steffen Beirle1, Nuria Benavent4, Alexander Borovski5, Ilya Bruchkouski6, Ka Lok Chan7,8, Sebastian Donner1, Theano Drosoglou3, Henning Finkenzeller9,10, Martina M. Friedrich11, Udo Frie&szlig;12, David Garcia-Nieto4, Laura G&oacute;mez-Mart&iacute;n13, Fran&ccedil;ois Hendrick11, Andreas Hilboll14, Junli Jin15, Paul Johnston16, Theodore K. Koenig9,10, Karin Kreher17, Vinod Kumar1, Aleksandra Kyuberis18, Johannes Lampel12,19, Cheng Liu20, Haoran Liu20, Jianzhong Ma21, Oleg L. Polyansky18,22, Oleg Postylyakov5, Richard Querel16, Alfonso Saiz-Lopez4, Stefan Schmitt12, Xin Tian23,24, Jan-Lukas Tirpitz12, Michel Van Roozendael11, Rainer Volkamer9,10, Zhuoru Wang8, Pinhua Xie24, Chengzhi Xing25, Jin Xu24, Margarita Yela13, Chengxin Zhang25, and Thomas Wagner11Max Planck Institute for Chemistry, Mainz, Germany 2Royal Netherlands Meteorological Institute (KNMI), De Bilt, the Netherlands 3Laboratory of Atmospheric Physics, Aristotle University of Thessaloniki, Thessaloniki, Greece 4Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Rocasolano (CSIC), Madrid, Spain 5A. M. Obukhov Institute of Atmospheric Physics, Russian Academy of Sciences, Moscow, Russia 6National Ozone Monitoring Research and Education Center BSU (NOMREC BSU), Belarusian State University, Minsk, Belarus 7Meteorologisches Institut, Ludwig-Maximilians-Universit&auml;t M&uuml;nchen, Munich, Germany 8Remote Sensing Technology Institute, German Aerospace Center (DLR), Oberpfaffenhofen, Germany 9Department of Chemistry, University of Colorado Boulder, Boulder, CO, USA 10Cooperative Institute for Research in Environmental Sciences, Boulder, CO, USA 11Royal Belgian Institute for Space Aeronomy, Brussels, Belgium 12Institute of Environmental Physics, University of Heidelberg, Heidelberg, Germany 13National Institute of Aerospatial Technology, Madrid, Spain 14Institute of Environmental Physics, University of Bremen, Bremen, Germany 15Meteorological Observation Center, China Meteorological Administration, Beijing, China 16National Institute of Water &amp; Atmospheric Research (NIWA), Lauder, New Zealand 17BK Scientific, Mainz, Germany 18Institute of Applied Physics, Russian Academy of Sciences, Nizhny Novgorod, Russia 19Airyx GmbH, Justus-von-Liebig-Str. 14, 69214 Eppelheim, Germany 20Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, Anhui, China 21Chinese Academy of Meteorology Science, China Meteorological Administration, Beijing, China 22Department of Physics and Astronomy, University College London, Gower St, London, WC1E 6BT, UK 23Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, China 24Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Hefei, China 25School of Earth and Space Sciences, University of Science and Technology of China, Hefei, Anhui, China </ul

Garcinol from Garcinia indica inhibits HIV-1 reverse transcriptase-associated ribonuclease H

The bioactive components of Garcinia indica, garcinol (camboginol), and isogarcinol (cambogin), are suitable drug candidates for the treatment of various human diseases. HIV-1-RNase H assay was used to study the RNase H inhibition by garcinol and isogarcinol. Docking of garcinol into the active site of the enzyme was carried out to rationalize the difference in activities between the two compounds. Garcinol showed higher HIV-1-RNase H inhibition than the known inhibitor RDS1759 and retained full potency against the RNase H of a drug-resistant HIV-1 reverse transcriptase form. Isogarcinol was distinctly less active than garcinol, indicating the importance of the enolizable β-diketone moiety of garcinol for anti-RNase H activity. Docking calculations confirmed these findings and suggested this moiety to be involved in the chelation of metal ions of the active site. On the basis of its HIV-1 reverse transcriptase-associated RNase H inhibitory activity, garcinol is worth being further explored concerning its potential as a cost-effective treatment for HIV patients

ProteinsPlus: a web portal for structure analysis of macromolecules

With currently more than 126 000 publicly available structures and an increasing growth rate, the Protein Data Bank constitutes a rich data source for structure-driven research in fields like drug discovery, crop science and biotechnology in general. Typical workflows in these areas involve manifold computational tools for the analysis and prediction of molecular functions. Here, we present the ProteinsPlus web server that offers a unified easy-to-use interface to a broad range of tools for the early phase of structure-based molecular modeling. This includes solutions for commonly required pre- processing tasks like structure quality assessment (EDIA), hydrogen placement (Protoss) and the search for alternative conformations (SIENA). Beyond that, it also addresses frequent problems as the generation of 2D-interaction diagrams (PoseView), protein–protein interface classification (HyPPI) as well as automatic pocket detection and druggablity assessment (DoGSiteScorer). The unified ProteinsPlus interface covering all featured approaches provides various facilities for intuitive input and result visualization, case-specific parameterization and download options for further processing. Moreover, its generalized workflow allows the user a quick familiarization with the different tools. ProteinsPlus also stores the calculated results temporarily for future request and thus facilitates convenient result communication and re-access. The server is freely available at http://proteins.plus

Airborne MAX-DOAS Measurements Over California: Testing the NASA OMI Tropospheric NO2 Product

Airborne Multi-AXis Differential Optical Absorption Spectroscopy (AMAX-DOAS) measurements of NO2 tropospheric vertical columns were performed over California for two months in summer 2010. The observations are compared to the NASA Ozone Monitoring Instrument (OMI) tropospheric vertical columns (data product v2.1) in two ways: (1) Median data were compared for the whole time period for selected boxes, and the agreement was found to be fair (R = 0.97, slope = 1.4 +/- 0.1, N= 10). (2) A comparison was performed on the mean of coincident AMAX-DOAS measurements within the area of the corresponding OMI pixels with the tropospheric NASA OMI NO2 assigned to that pixel. The effects of different data filters were assessed. Excellent agreement and a strong correlation (R = 0.85, slope = 1.05 +/- 0.09, N= 56) was found for (2) when the data were filtered to eliminate large pixels near the edge of the OMI orbit, the cloud radiance fraction was2 km, and a representative sample of the footprint was taken by the AMAX-DOAS instrument. The AMAX-DOAS and OMI data sets both show a reduction of NO2 tropospheric columns on weekends by 38 +/- 24% and 33 +/- 11%, respectively. The assumptions in the tropospheric satellite air mass factor simulations were tested using independent measurements of surface albedo, aerosol extinction, and NO2 profiles for Los Angeles for July 2010 indicating an uncertainty of 12%

First detection of ammonia (NH₃) in the Asian summer monsoon upper troposphere

Ammonia (NH3) has been detected in the upper troposphere by the analysis of averaged MIPAS (Michelson Interferometer for Passive Atmospheric Sounding) infrared limb-emission spectra. We have found enhanced amounts of NH3 within the region of the Asian summer monsoon at 12–15 km altitude. Three-monthly, 10° longitude  ×  10° latitude average profiles reaching maximum mixing ratios of around 30 pptv in this altitude range have been retrieved, with a vertical resolution of 3–8 km and estimated errors of about 5 pptv. These observations show that loss processes during transport from the boundary layer to the upper troposphere within the Asian monsoon do not deplete the air entirely of NH3. Thus, ammonia might contribute to the so-called Asian tropopause aerosol layer by the formation of ammonium aerosol particles. On a global scale, outside the monsoon area and during different seasons, we could not detect enhanced values of NH3 above the actual detection limit of about 3–5 pptv. This upper bound helps to constrain global model simulations