Biomass burning plume chemistry: OH-radical-initiated oxidation of 3-penten-2-one and its main oxidation product 2-hydroxypropanal

Abstract. In order to enlarge our understanding of biomass burning plume chemistry, the OH radical initiated oxidation of 3-penten-2-one (3P2), identified in biomass burning emissions, and 2-hydroxypropanal (2HPr) were investigated at 298 ± 3 K and 990 ± 15 mbar in two atmospheric simulation chambers using long-path FTIR spectroscopy. The rate coefficient of 3P2 + OH was determined to be (6.2 ± 1.0) × 10−11 cm3 molecule−1 s−1 and the molar first-generation yields for acetaldehyde, methyl glyoxal, 2HPr and the sum of PAN and CO2, used to determine the CH3C(O) radical yield, were 0.39 ± 0.07, 0.32 ± 0.08, 0.68 ± 0.27, and 0.56 ± 0.14, respectively, under conditions where the 3P2 derived peroxy radicals react solely with NO. The 2HPr + OH reaction was investigated using 3P2 + OH as a source of the α-hydroxyaldehyde adjusting the experimental conditions to shift the reaction system towards secondary oxidation processes. The rate coefficient was estimated to be (2.2 ± 0.6) × 10−11 cm3 molecule−1 s−1. Employing an Euler-Cauchy model to describe the temporal behaviour of the experiments, the further oxidation of 2HPr was shown to form methyl glyoxal, acetaldehyde and CO2 with estimated yields of 0.21 ± 0.05, 0.79 ± 0.05, and 0.79 ± 0.05, respectively.

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Modelling of the photooxidation of toluene: conceptual ideas for validating detailed mechanisms

Atmospheric Chemistry and Physics ◽

10.5194/acp-3-89-2003 ◽

2003 ◽

Vol 3 (1) ◽

pp. 89-106 ◽

Cited By ~ 41

Author(s):

V. Wagner ◽

M. E. Jenkin ◽

S. M. Saunders ◽

J. Stanton ◽

K Wirtz ◽

...

Keyword(s):

First Generation ◽

Chemical Mechanism ◽

Ozone Production ◽

Peroxy Radicals ◽

Reaction Systems ◽

Master Chemical Mechanism ◽

Reactive Nitrogen Oxides ◽

Toluene Photooxidation ◽

Radical Transformation ◽

Validation Experiments

Abstract. Toluene photooxidation is chosen as an example to examine how simulations of smog-chamber experiments can be used to unravel shortcomings in detailed mechanisms and to provide information on complex reaction systems that will be crucial for the design of future validation experiments. The mechanism used in this study is extracted from the Master Chemical Mechanism Version 3 (MCM v3) and has been updated with new modules for cresol and g-dicarbonyl chemistry. Model simulations are carried out for a toluene-NOx experiment undertaken at the European Photoreactor (EUPHORE). The comparison of the simulation with the experimental data reveals two fundamental shortcomings in the mechanism: OH production is too low by about 80%, and the ozone concentration at the end of the experiment is over-predicted by 55%. The radical budget was analysed to identify the key intermediates governing the radical transformation in the toluene system. Ring-opening products, particularly conjugated g-dicarbonyls, were identified as dominant radical sources in the early stages of the experiment. The analysis of the time evolution of radical production points to a missing OH source that peaks when the system reaches highest reactivity. First generation products are also of major importance for the ozone production in the system. The analysis of the radical budget suggests two options to explain the concurrent under-prediction of OH and over-prediction of ozone in the model: 1) missing oxidation processes that produce or regenerate OH without or with little NO to NO2 conversion or 2) NO3 chemistry that sequesters reactive nitrogen oxides into stable nitrogen compounds and at the same time produces peroxy radicals. Sensitivity analysis was employed to identify significant contributors to ozone production and it is shown how this technique, in combination with ozone isopleth plots, can be used for the design of validation experiments.

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Evolution of NO3 reactivity during the oxidation of isoprene

10.5194/acp-2020-360 ◽

2020 ◽

Author(s):

Patrick Dewald ◽

Jonathan M. Liebmann ◽

Nils Friedrich ◽

Justin Shenolikar ◽

Jan Schuladen ◽

...

Keyword(s):

Rate Coefficient ◽

Chemical Mechanism ◽

Organic Nitrates ◽

Peroxy Radicals ◽

Reaction Products ◽

Flow Tube ◽

Mixing Ratios ◽

Tube Reactor ◽

Master Chemical Mechanism ◽

Series Of Experiments

Abstract. In a series of experiments in an atmospheric simulation chamber (SAPHIR, Forschungszentrum Jülich, Germany) NO3 reactivity (kNO3) resulting from the reaction of NO3 with isoprene and stable trace gases formed as products was measured directly using a flow-tube reactor coupled to a cavity-ring-down spectrometer (FT-CRDS). The experiments were carried out in both dry and humid air with variation of the initial mixing ratios of ozone (50–100 ppbv), isoprene (3–22 ppbv) and NO2 (5–30 ppbv). kNO3 was in excellent agreement with values calculated from the isoprene mixing ratio and the rate coefficient for the reaction of NO3 with isoprene. This result serves both to confirm that the FT-CRDS returns accurate values of kNO3 even at elevated NO2 concentrations and to show that reactions of NO3 with stable reaction products like non-radical organic nitrates do not contribute significantly to NO3 reactivity during the oxidation of isoprene. A comparison of kNO3 with NO3 reactivities calculated from NO3 mixing ratios and NO3 production rates suggests that organic peroxy radicals and HO2 account for ~ 50 % of NO3 losses. This contradicts predictions based on numerical simulations using the Master Chemical Mechanism (MCM version 3.3.1) unless the rate coefficient for reaction between NO3 and isoprene-derived RO2 is roughly doubled to ≈ 5 × 10−12 cm3 molecule−1 s−1.

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Highly oxygenated organic molecule (HOM) formation in the isoprene oxidation by NO3 radical

Atmospheric Chemistry and Physics ◽

10.5194/acp-21-9681-2021 ◽

2021 ◽

Vol 21 (12) ◽

pp. 9681-9704

Author(s):

Defeng Zhao ◽

Iida Pullinen ◽

Hendrik Fuchs ◽

Stephanie Schrade ◽

Rongrong Wu ◽

...

Keyword(s):

Double Bond ◽

First Generation ◽

Second Generation ◽

Closed Shell ◽

Time Profile ◽

Direct Reaction ◽

Peroxy Radicals ◽

Experimental Conditions ◽

Time Profiles ◽

Carbon Double Bond

Abstract. Highly oxygenated organic molecules (HOM) are found to play an important role in the formation and growth of secondary organic aerosol (SOA). SOA is an important type of aerosol with significant impact on air quality and climate. Compared with the oxidation of volatile organic compounds by ozone (O3) and hydroxyl radical (OH), HOM formation in the oxidation by nitrate radical (NO3), an important oxidant at nighttime and dawn, has received less attention. In this study, HOM formation in the reaction of isoprene with NO3 was investigated in the SAPHIR chamber (Simulation of Atmospheric PHotochemistry In a large Reaction chamber). A large number of HOM, including monomers (C5), dimers (C10), and trimers (C15), both closed-shell compounds and open-shell peroxy radicals (RO2), were identified and were classified into various series according to their formula. Their formation pathways were proposed based on the peroxy radicals observed and known mechanisms in the literature, which were further constrained by the time profiles of HOM after sequential isoprene addition to differentiate first- and second-generation products. HOM monomers containing one to three N atoms (1–3N-monomers) were formed, starting with NO3 addition to carbon double bond, forming peroxy radicals, followed by autoxidation. 1N-monomers were formed by both the direct reaction of NO3 with isoprene and of NO3 with first-generation products. 2N-monomers (e.g., C5H8N2On(n=7–13), C5H10N2On(n=8–14)) were likely the termination products of C5H9N2On⚫, which was formed by the addition of NO3 to C5-hydroxynitrate (C5H9NO4), a first-generation product containing one carbon double bond. 2N-monomers, which were second-generation products, dominated in monomers and accounted for ∼34 % of all HOM, indicating the important role of second-generation oxidation in HOM formation in the isoprene + NO3 reaction under our experimental conditions. H shift of alkoxy radicals to form peroxy radicals and subsequent autoxidation (“alkoxy–peroxy” pathway) was found to be an important pathway of HOM formation. HOM dimers were mostly formed by the accretion reaction of various HOM monomer RO2 and via the termination reactions of dimer RO2 formed by further reaction of closed-shell dimers with NO3 and possibly by the reaction of C5–RO2 with isoprene. HOM trimers were likely formed by the accretion reaction of dimer RO2 with monomer RO2. The concentrations of different HOM showed distinct time profiles during the reaction, which was linked to their formation pathway. HOM concentrations either showed a typical time profile of first-generation products, second-generation products, or a combination of both, indicating multiple formation pathways and/or multiple isomers. Total HOM molar yield was estimated to be 1.2 %-0.7%+1.3%, which corresponded to a SOA yield of ∼3.6 % assuming the molecular weight of C5H9NO6 as the lower limit. This yield suggests that HOM may contribute a significant fraction to SOA yield in the reaction of isoprene with NO3.

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Modelling of the photooxidation of toluene: conceptual ideas for validating detailed mechanisms

Atmospheric Chemistry and Physics Discussions ◽

10.5194/acpd-2-1217-2002 ◽

2002 ◽

Vol 2 (4) ◽

pp. 1217-1259 ◽

Cited By ~ 1

Author(s):

V. Wagner ◽

M. E. Jenkin ◽

S. M. Saunders ◽

J. Stanton ◽

K. Wirtz ◽

...

Keyword(s):

First Generation ◽

Chemical Mechanism ◽

Ozone Production ◽

Peroxy Radicals ◽

Reaction Systems ◽

Master Chemical Mechanism ◽

Reactive Nitrogen Oxides ◽

Toluene Photooxidation ◽

Radical Transformation ◽

Validation Experiments

Abstract. Toluene photooxidation is chosen as an example to examine how simulations of smog-chamber experiments can be used to unravel shortcomings in detailed mechanisms and to provide information on complex reaction systems that will be crucial for the design of future validation experiments. The mechanism used in this study is extracted from the Master Chemical Mechanism Version 3 (MCM v3) and has been updated with new modules for cresol and g-dicarbonyl chemistry. Model simulations are carried out for a toluene-NOx experiment undertaken at the European Photoreactor (EUPHORE). The comparison of the simulation with the experimental data reveals two fundamental shortcomings in the mechanism: OH production is too low by about 80%, and the ozone concentration at the end of the experiment is over-predicted by 55%. The radical budget was analysed to identify the key intermediates governing the radical transformation in the toluene system. Ring-opening products, particularly conjugated g-dicarbonyls, were identified as dominant radical sources in the early stages of the experiment. The analysis of the time evolution of radical production points to a missing OH source that peaks when the system reaches highest reactivity. First generation products are also of major importance for the ozone production in the system. The analysis of the radical budget suggests two options to explain the concurrent under-prediction of OH and over-prediction of ozone in the model: 1) missing oxidation processes that produce or regenerate OH without or with little NO to NO2 conversion or 2) NO3 chemistry that sequesters reactive nitrogen oxides into stable nitrogen compounds and at the same time produces peroxy radicals. Sensitivity analysis was employed to identify significant contributors to ozone production and it is shown how this technique, in combination with ozone isopleth plots, can be used for the design of validation experiments.

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Evolution of NO3 reactivity during the oxidation of isoprene

Atmospheric Chemistry and Physics ◽

10.5194/acp-20-10459-2020 ◽

2020 ◽

Vol 20 (17) ◽

pp. 10459-10475

Author(s):

Patrick Dewald ◽

Jonathan M. Liebmann ◽

Nils Friedrich ◽

Justin Shenolikar ◽

Jan Schuladen ◽

...

Keyword(s):

Rate Coefficient ◽

Chemical Mechanism ◽

Organic Nitrates ◽

Peroxy Radicals ◽

Reaction Products ◽

Flow Tube ◽

Mixing Ratios ◽

Tube Reactor ◽

Master Chemical Mechanism ◽

Series Of Experiments

Abstract. In a series of experiments in an atmospheric simulation chamber (SAPHIR,1 Forschungszentrum Jülich, Germany), NO3 reactivity (kNO3) resulting from the reaction of NO3 with isoprene and stable trace gases formed as products was measured directly using a flow tube reactor coupled to a cavity ring-down spectrometer (FT-CRDS). The experiments were carried out in both dry and humid air with variation of the initial mixing ratios of ozone (50–100 ppbv), isoprene (3–22 ppbv) and NO2 (5–30 ppbv). kNO3 was in excellent agreement with values calculated from the isoprene mixing ratio and the rate coefficient for the reaction of NO3 with isoprene. This result serves to confirm that the FT-CRDS returns accurate values of kNO3 even at elevated NO2 concentrations and to show that reactions of NO3 with stable reaction products like non-radical organic nitrates do not contribute significantly to NO3 reactivity during the oxidation of isoprene. A comparison of kNO3 with NO3 reactivities calculated from NO3 mixing ratios and NO3 production rates suggests that organic peroxy radicals and HO2 account for ∼50 % of NO3 losses. This contradicts predictions based on numerical simulations using the Master Chemical Mechanism (MCM version 3.3.1) unless the rate coefficient for reaction between NO3 and isoprene-derived RO2 is roughly doubled to ∼5×10-12 cm3 molecule−1 s−1.

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Comprehensive modeling of bloodstain aging by multivariate Raman spectral resolution with kinetics

Communications Chemistry ◽

10.1038/s42004-019-0217-1 ◽

2019 ◽

Vol 2 (1) ◽

Cited By ~ 1

Author(s):

Ayari Takamura ◽

Daisuke Watanabe ◽

Rintaro Shimada ◽

Takeaki Ozawa

Keyword(s):

Spectral Resolution ◽

Aging Process ◽

Near Infrared ◽

Biochemical Characterization ◽

Forensic Analysis ◽

Chemical Mechanism ◽

Experimental Conditions ◽

Spectral Components ◽

Different Temperatures ◽

Analytical Approaches

Abstract Blood, as a cardinal biological system, is a challenging target for biochemical characterization because of sample complexity and a lack of analytical approaches. To reveal and evaluate aging process of blood compositions is an unexplored issue in forensic analysis, which is useful to elucidate the details of a crime. Here we demonstrate a spectral deconvolution model of near-infrared Raman spectra of bloodstain to comprehensively describe the aging process based on the chemical mechanism, particularly the kinetics. The bloodstain spectra monitored over several months at different temperatures are decomposed into significant spectral components by multivariate calculation. The kinetic schemes of the spectral components are explored and subsequently incorporated into the developed algorithm for the optimal spectral resolution. Consequently, the index of bloodstain aging is proposed, which can be used under different experimental conditions. This work provides a novel perspective on the chemical mechanisms in bloodstain aging and facilitates forensic applications.

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Glucuronides Hydrolysis by Intestinal Microbial β-Glucuronidases (GUS) Is Affected by Sampling, Enzyme Preparation, Buffer pH, and Species

Pharmaceutics ◽

10.3390/pharmaceutics13071043 ◽

2021 ◽

Vol 13 (7) ◽

pp. 1043

Author(s):

Christabel Ebuzoeme ◽

Imoh Etim ◽

Autumn Ikimi ◽

Jamie Song ◽

Ting Du ◽

...

Keyword(s):

Enzyme Preparation ◽

Reaction System ◽

Reaction Rates ◽

Experimental Conditions ◽

Model Animal ◽

Fresh Feces ◽

Time Buffer ◽

Exogenous Compounds ◽

Activity Loss ◽

The Impact

Glucuronides hydrolysis by intestinal microbial β-Glucuronidases (GUS) is an important procedure for many endogenous and exogenous compounds. The purpose of this study is to determine the impact of experimental conditions on glucuronide hydrolysis by intestinal microbial GUS. Standard probe 4-Nitrophenyl β-D-glucopyranoside (pNPG) and a natural glucuronide wogonoside were used as the model compounds. Feces collection time, buffer conditions, interindividual, and species variations were evaluated by incubating the substrates with enzymes. The relative reaction activity of pNPG, reaction rates, and reaction kinetics for wogonoside were calculated. Fresh feces showed the highest hydrolysis activities. Sonication increased total protein yield during enzyme preparation. The pH of the reaction system increased the activity in 0.69–1.32-fold, 2.9–12.9-fold, and 0.28–1.56-fold for mouse, rat, and human at three different concentrations of wogonoside, respectively. The Vmax for wogonoside hydrolysis was 2.37 ± 0.06, 4.48 ± 0.11, and 5.17 ± 0.16 μmol/min/mg and Km was 6.51 ± 0.71, 3.04 ± 0.34, and 0.34 ± 0.047 μM for mouse, rat, and human, respectively. The inter-individual difference was significant (4–6-fold) using inbred rats as the model animal. Fresh feces should be used to avoid activity loss and sonication should be utilized in enzyme preparation to increase hydrolysis activity. The buffer pH should be appropriate according to the species. Inter-individual and species variations were significant.

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Comparisons of observed and modeled OH and HO2concentrations during the ambient measurement period of the HOxComp field campaign

Atmospheric Chemistry and Physics ◽

10.5194/acp-12-2567-2012 ◽

2012 ◽

Vol 12 (5) ◽

pp. 2567-2585 ◽

Cited By ~ 23

Author(s):

Y. Kanaya ◽

A. Hofzumahaus ◽

H.-P. Dorn ◽

T. Brauers ◽

H. Fuchs ◽

...

Keyword(s):

Atmospheric Chemistry ◽

Chemical Mechanism ◽

Ozone Production ◽

High Yield ◽

Base Case ◽

Peroxy Radicals ◽

Field Campaign ◽

Mixing Ratios ◽

Measurement Mode ◽

Single Instrument

Abstract. A photochemical box model constrained by ancillary observations was used to simulate OH and HO2 concentrations for three days of ambient observations during the HOxComp field campaign held in Jülich, Germany in July 2005. Daytime OH levels observed by four instruments were fairly well reproduced to within 33% by a base model run (Regional Atmospheric Chemistry Mechanism with updated isoprene chemistry adapted from Master Chemical Mechanism ver. 3.1) with high R2 values (0.72–0.97) over a range of isoprene (0.3–2 ppb) and NO (0.1–10 ppb) mixing ratios. Daytime HO2(*) levels, reconstructed from the base model results taking into account the sensitivity toward speciated RO2 (organic peroxy) radicals, as recently reported from one of the participating instruments in the HO2 measurement mode, were 93% higher than the observations made by the single instrument. This also indicates an overprediction of the HO2 to OH recycling. Together with the good model-measurement agreement for OH, it implies a missing OH source in the model. Modeled OH and HO2(*) could only be matched to the observations by addition of a strong unknown loss process for HO2(*) that recycles OH at a high yield. Adding to the base model, instead, the recently proposed isomerization mechanism of isoprene peroxy radicals (Peeters and Müller, 2010) increased OH and HO2(*) by 28% and 13% on average. Although these were still only 4% higher than the OH observations made by one of the instruments, larger overestimations (42–70%) occurred with respect to the OH observations made by the other three instruments. The overestimation in OH could be diminished only when reactive alkanes (HC8) were solely introduced to the model to explain the missing fraction of observed OH reactivity. Moreover, the overprediction of HO2(*) became even larger than in the base case. These analyses imply that the rates of the isomerization are not readily supported by the ensemble of radical observations. One of the measurement days was characterized by low isoprene concentrations (∼0.5 ppb) and OH reactivity that was well explained by the observed species, especially before noon. For this selected period, as opposed to the general behavior, the model tended to underestimate HO2(*). We found that this tendency is associated with high NOx concentrations, suggesting that some HO2 production or regeneration processes under high NOx conditions were being overlooked; this might require revision of ozone production regimes.

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Investigating the NO-dependent photooxidation of limonene by OH and O3 using the atmosphere simulation chamber SAPHIR

10.5194/egusphere-egu21-11130 ◽

2021 ◽

Author(s):

Yat Sing Pang ◽

Martin Kaminski ◽

Anna Novelli ◽

Philip Carlsson ◽

Ismail-Hakki Acir ◽

...

Keyword(s):

Organic Aerosol ◽

Oxidation Products ◽

Chemical Mechanism ◽

Reaction Pathways ◽

Oh Radicals ◽

Oh Radical ◽

Simulation Experiments ◽

Master Chemical Mechanism ◽

Simulation Results ◽

Atmosphere Simulation Chamber

Limonene is the fourth-most abundant monoterpene in the atmosphere, which upon oxidation leads to the formation of secondary organic aerosol (SOA) and thereby influences climate and air quality.In this study, the oxidation of limonene by OH at different atmospherically relevant NO and HO2 levels (NO: 0.1 &#8211; 10 ppb; HO2: 20 ppt) was investigated in simulation experiments in the SAPHIR chamber at Forschungszentrum J&#252;lich. The analysis focuses on comparing measured radical concentrations (RO2, HO2, OH) and OH reactivity (kOH) with modeled values calculated using the Master Chemical Mechanism (MCM) version 3.3.1.At high and medium NO concentrations, RO2 is expected to quickly react with NO. An HO2 radical is produced during the process that can be converted back to an OH radical by another reaction with NO. Consistently, for experiments conducted at medium NO levels (~0.5 ppb, RO2 lifetime ~10 s), simulated RO2, HO2, and OH agree with observations within the measurement uncertainties, if the OH reactivity of oxidation products is correctly described.At lower NO concentrations, the regeneration of HO2 in the RO2 + NO reaction is slow and the reaction of RO2 with HO2 gains importance in forming peroxides. However, simulation results show a large discrepancy between calculated radical concentrations and measurements at low NO levels (<0.1 ppb, RO2 lifetime ~ 100 s). Simulated RO2 concentrations are found to be overestimated by a factor of three; simulated HO2 concentrations are underestimated by 50 %; simulated OH concentrations are underestimated by about 35%, even if kOH is correctly described. This suggests that there could be additional RO2 reaction pathways that regenerate HO2 and OH radicals become important, but they are not taken into account in the MCM model.

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Biomass burning plume chemistry: OH-radical-initiated oxidation of 3-penten-2-one and its main oxidation product 2-hydroxypropanal