Alpha-pinene oxidation by OH: simulations of laboratory experiments

Abstract. This paper presents a state-of-the-art gas-phase mechanism for the degradation of α-pinene by OH and its validation by box model simulations of laboratory measurements. It is based on the near-explicit mechanisms for the oxidation of α-pinene and pinonaldehyde by OH proposed by Peeters and co-workers. The extensive set of α-pinene photooxidation experiments performed in presence as well as in absence of NO by Nozière et al. (1999a) is used to test the mechanism. The comparison of the calculated vs measured concentrations as a function of time shows that the levels of OH, NO, NO2 and light are well reproduced in the model. Noting the large scatter in the experimental results as well as the difficulty to retrieve true product yields from concentrations data, a methodology is proposed for comparing the model and the data. The model succeeds in reproducing the average apparent yields of pinonaldehyde, acetone, total nitrates and total PANs in the experiments performed in presence of NO. In absence of NO, pinonaldehyde is fairly well reproduced, but acetone is largely underestimated. The dependence of the product yields on the concentration of NO and α-pinene is investigated, with a special attention on the influence of the multiple competitions of reactions affecting the peroxy radicals in the mechanism. We show that the main oxidation channels differ largely according to photochemical conditions. E.g. the pinonaldehyde yield is estimated to be about 10% in the remote atmosphere and up to 60% in very polluted areas. We stress the need for additional theoretical/laboratory work to unravel the chemistry of the primary products as well as the ozonolysis and nitrate-initiated oxidation of α-pinene.

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Alpha-pinene oxidation by OH: simulations of laboratory experiments

Atmospheric Chemistry and Physics Discussions ◽

10.5194/acpd-4-4039-2004 ◽

2004 ◽

Vol 4 (4) ◽

pp. 4039-4103 ◽

Cited By ~ 1

Author(s):

M. Capouet ◽

J. Peeters ◽

B. Nozière ◽

J.-F. Müller

Keyword(s):

Gas Phase ◽

Laboratory Experiments ◽

State Of The Art ◽

Peroxy Radicals ◽

Large Scatter ◽

Laboratory Measurements ◽

Model Simulations ◽

Product Yields ◽

Alpha Pinene ◽

Primary Products

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Application of chemical derivatization techniques combined with chemical ionization mass spectrometry to detect stabilized Criegee intermediates and peroxy radicals in the gas phase

Atmospheric Measurement Techniques ◽

10.5194/amt-14-2501-2021 ◽

2021 ◽

Vol 14 (3) ◽

pp. 2501-2513

Author(s):

Alexander Zaytsev ◽

Martin Breitenlechner ◽

Anna Novelli ◽

Hendrik Fuchs ◽

Daniel A. Knopf ◽

...

Keyword(s):

Gas Phase ◽

Chemical Ionization ◽

Laboratory Experiments ◽

Spin Trapping ◽

Integration Time ◽

Ionization Mass ◽

Peroxy Radicals ◽

Chemical Derivatization ◽

Spin Traps ◽

Criegee Intermediates

Abstract. Short-lived highly reactive atmospheric species, such as organic peroxy radicals (RO2) and stabilized Criegee intermediates (SCIs), play an important role in controlling the oxidative removal and transformation of many natural and anthropogenic trace gases in the atmosphere. Direct speciated measurements of these components are extremely helpful for understanding their atmospheric fate and impact. We describe the development of an online method for measurements of SCIs and RO2 in laboratory experiments using chemical derivatization and spin trapping techniques combined with H3O+ and NH4+ chemical ionization mass spectrometry (CIMS). Using chemical derivatization agents with low proton affinity, such as electron-poor carbonyls, we scavenge all SCIs produced from a wide range of alkenes without depleting CIMS reagent ions. Comparison between our measurements and results from numeric modeling, using a modified version of the Master Chemical Mechanism, shows that the method can be used for the quantification of SCIs in laboratory experiments with a detection limit of 1.4×107 molecule cm−3 for an integration time of 30 s with the instrumentation used in this study. We show that spin traps are highly reactive towards atmospheric radicals and form stable adducts with them by studying the gas-phase kinetics of the reaction of spin traps with the hydroxyl radical (OH). We also demonstrate that spin trap adducts with SCIs and RO2 can be simultaneously probed and quantified under laboratory conditions with a detection limit of 1.6×108 molecule cm−3 for an integration time of 30 s for RO2 species with the instrumentation used in this study. Spin trapping prevents radical secondary reactions and cycling, ensuring that measurements are not biased by chemical interferences, and it can be implemented for detecting RO2 species in laboratory studies and potentially in the ambient atmosphere.

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Investigating monoterpene ozonolysis reactions in the mobile DouAir atmospheric simulation chamber: field and laboratory experiments

10.5194/egusphere-egu21-14892 ◽

2021 ◽

Author(s):

Ahmad Lahib ◽

Hichem Bouzidi ◽

Nina Reijrink ◽

Marius Duncianu ◽

Emilie Perraudin ◽

...

Keyword(s):

Volatile Organic Compounds ◽

Organic Compounds ◽

Laboratory Experiments ◽

Peroxy Radical ◽

Chemical Transformations ◽

Peroxy Radicals ◽

Model Simulations ◽

Chemical Mechanisms ◽

Volatile Organic ◽

Biogenic Compounds

The chemistry of the atmosphere is usually studied using three different approaches, i.e. field measurements, laboratory studies and chemical model calculations. All three are complementary and powerful means to investigate chemical transformations of pollutants and improve our understanding of the atmosphere. Atmospheric simulation chambers are one of the most direct and critical approaches to mimic and examine chemical transformations under controlled experimental conditions. In combination with box model simulations, they allow assessment of the accuracy of chemical mechanisms implemented in atmospheric models.During the CERVOLAND field campaign (Characterisation of Emissions and Reactivity of Volatile Organic compounds in the LANDes forest) we deployed a new mobile atmospheric chamber (DouAir) to probe the oxidation of biogenic volatile organic compounds (BVOCs) in real air masses. Biogenic compounds emitted by the surrounding forest (mainly pines - (Maritime pine, Pinus pinaster Ait) were trapped in DouAir and their transformations were probed using state-of-the-art online instrumentation, including PTR-ToF-MS (VOCs), PERCA (peroxy radicals), O3 and NOx analysers, and SMPS (aerosols).The objectives of the present study were to (1) reproduce in the laboratory selected field experiments performed during CERVOLAND, the chemical composition of the air mass being simplified, and (2) compare both the field and laboratory results to 0-D box model simulations using the Master Chemical Mechanisms (MCM). Comparing field observations, laboratory experiments and model simulations provides a critical test of our understanding of atmospheric oxidation processes involving biogenic compounds.Here, we present ozonolysis experiments of primary biogenic VOCs (mainly monoterpenes) under dark conditions. Initial conditions used for the laboratory experiments were derived from reactant concentrations trapped in DouAir during CERVOLAND. The results show the capability of the model to reproduce oxidation rates of primary VOCs within uncertainty, although the model considerably overestimates measured peroxy radical concentrations. The addition of rapid self- and cross-reactions of monoterpene-derived peroxy radicals in the MCM improves the agreement with the measured peroxy radical concentrations.

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Application of chemical derivatization techniques combined with chemical ionization mass spectrometry to detect stabilized Criegee intermediates and peroxy radicals in the gas phase

10.5194/amt-2020-335 ◽

2020 ◽

Cited By ~ 1

Author(s):

Alexander Zaytsev ◽

Martin Breitenlechner ◽

Anna Novelli ◽

Hendrik Fuchs ◽

Daniel A. Knopf ◽

...

Keyword(s):

Gas Phase ◽

Chemical Ionization ◽

Laboratory Experiments ◽

Spin Trapping ◽

Chemical Ionization Mass Spectrometry ◽

Integration Time ◽

Ionization Mass ◽

Peroxy Radicals ◽

Chemical Derivatization ◽

Criegee Intermediates

Abstract. Short-lived highly reactive atmospheric species, such as organic peroxy radicals (RO2) and stabilized Criegee intermediates (SCIs), play an important role in controlling the oxidative removal and transformation of many natural and anthropogenic trace gases in the atmosphere. Direct speciated measurements of these components are extremely helpful for understanding their atmospheric fate and impact. We describe the development of an online method for measurements of SCIs and RO2 in laboratory experiments using chemical derivatization and spin trapping techniques combined with H3O+ and NH4+ chemical ionization mass spectrometry (CIMS). Using chemical derivatization agents with low proton affinity, such as electron-poor carbonyls, we scavenge all SCIs produced from a wide range of alkenes without depleting CIMS reagent ions. Comparison between our measurements and results from numeric modelling, using a modified version of the Master Chemical Mechanism, shows that the method can be used for quantification of SCIs in laboratory experiments with detection limit of 1.4 × 107 molecule cm-3 for 30 s integration time with the instrumentation used in this study. We show that spin traps are highly reactive towards atmospheric radicals and form stable adducts with them by studying the gas-phase kinetics of their reaction with hydroxyl radical (OH). We also demonstrate that spin trap adducts with SCIs and RO2 can be simultaneously probed and quantified under laboratory conditions with detection limit of 1.6 × 108 molecule cm-3 for 30 s integration time for RO2 species with the instrumentation used in this study. Spin trapping prevents radical secondary reactions and cycling, which ensures that measurements are not biased by chemical interferences, and can be implemented for detecting RO2 species in the ambient atmosphere.

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Space and laboratory discovery of HC3S+

Astronomy and Astrophysics ◽

10.1051/0004-6361/202040013 ◽

2021 ◽

Vol 646 ◽

pp. L3 ◽

Cited By ~ 2

Author(s):

J. Cernicharo ◽

C. Cabezas ◽

Y. Endo ◽

N. Marcelino ◽

M. Agúndez ◽

...

Keyword(s):

Ab Initio Calculations ◽

Ab Initio ◽

Gas Phase ◽

State Of The Art ◽

Protonated Form ◽

Abundance Ratio ◽

Rotational Spectrum ◽

Laboratory Measurements ◽

Upper Limit ◽

Phase Chemical

We report the detection in TMC-1 of the protonated form of C3S. The discovery of the cation HC3S+ was carried through the observation of four harmonically related lines in the Q band using the Yebes 40 m radiotelescope, and is supported by accurate ab initio calculations and laboratory measurements of its rotational spectrum. We derive a column density N(HC3S+) = (2.0 ± 0.5)×1011 cm−2, which translates to an abundance ratio C3S/HC3S+ of 65 ± 20. This ratio is comparable to the CS/HCS+ ratio (35 ± 8) and is a factor of about ten larger than the C3O/HC3O+ ratio previously found in the same source. However, the abundance ratio HC3O+/HC3S+ is 1.0 ± 0.5, while C3O/C3S is just ∼0.11. We also searched for protonated C2S in TMC-1, based on ab initio calculations of its spectroscopic parameters, and derive a 3σ upper limit of N(HC2S+) ≤ 9 × 1011 cm−2 and a C2S/HC2S+ ≥ 60. The observational results are compared with a state-of-the-art gas-phase chemical model and conclude that HC3S+ is mostly formed through several pathways: proton transfer to C3S, reaction of S+ with c-C3H2, and reaction between neutral atomic sulfur and the ion C3H3+.

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Radiolysis of methylcyclopentane. III. Liquid phase mechanism and comparison of cycloalkanes

Canadian Journal of Chemistry ◽

10.1139/v68-536 ◽

1968 ◽

Vol 46 (20) ◽

pp. 3235-3240 ◽

Cited By ~ 11

Author(s):

Gordon R. Freeman ◽

E. Diane Stover

Keyword(s):

Liquid Phase ◽

Gas Phase ◽

Bond Cleavage ◽

Open Chain ◽

Methyl Substitution ◽

Product Yields ◽

Total Ionization ◽

Gamma Radiolysis ◽

G Value

The initial yields of the major products of the gamma radiolysis of liquid methylcyclopentane (MCP) at 25° are: G(H2) = 4.2, G(1-methylcyclopentene plus methylenecyclopentane) = 2.7, G(3- plus 4-methyl-cyclopentene) = 1.0, G(open chain hexene) = 1.0, and G(bimethylcyclopentyl) = 0.9. The effects of scavengers on the product yields are reported and the mechanism is discussed.The liquid phase radiolytic decompositions of cyclohexane (CH), methylcyclohexane (MCH), cyclopentane (CP), and MCP are compared. The net amount of C—C bond cleavage is much greater in the five-membered than in the six-membered rings. Methyl substitution on the ring reduces G(H2) by about one unit, mainly because of the formation of a type of ion (QH+) that does not yield hydrogen when neutralized by an electron. The QH+ type ions are formed in MCH and MCP, but not in CH and CP. In all the systems, another type of ion (N+) that does not yield hydrogen when neutralized by an electron is formed with a G value of about unity. The type of ion (PH+) that does yield hydrogen when neutralized by an electron has a G value of 3.4 in CH and CP, but only 2.0 in MCP. It is concluded that G(total ionization) is in the vicinity of 4.4 in the liquid compounds, virtually the same as the gas phase values.

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State-of-the-Art Native Mass Spectrometry and Ion Mobility Methods to Monitor Homogeneous Site-Specific Antibody-Drug Conjugates Synthesis

Pharmaceuticals ◽

10.3390/ph14060498 ◽

2021 ◽

Vol 14 (6) ◽

pp. 498

Author(s):

Evolène Deslignière ◽

Anthony Ehkirch ◽

Bastiaan L. Duivelshof ◽

Hanna Toftevall ◽

Jonathan Sjögren ◽

...

Keyword(s):

Mass Spectrometry ◽

Gas Phase ◽

Ion Mobility ◽

State Of The Art ◽

Native Mass Spectrometry ◽

Site Specific ◽

Drug Conjugates ◽

Conjugation Process ◽

Antibody Drug

Antibody-drug conjugates (ADCs) are biotherapeutics consisting of a tumor-targeting monoclonal antibody (mAb) linked covalently to a cytotoxic drug. Early generation ADCs were predominantly obtained through non-selective conjugation methods based on lysine and cysteine residues, resulting in heterogeneous populations with varying drug-to-antibody ratios (DAR). Site-specific conjugation is one of the current challenges in ADC development, allowing for controlled conjugation and production of homogeneous ADCs. We report here the characterization of a site-specific DAR2 ADC generated with the GlyCLICK three-step process, which involves glycan-based enzymatic remodeling and click chemistry, using state-of-the-art native mass spectrometry (nMS) methods. The conjugation process was monitored with size exclusion chromatography coupled to nMS (SEC-nMS), which offered a straightforward identification and quantification of all reaction products, providing a direct snapshot of the ADC homogeneity. Benefits of SEC-nMS were further demonstrated for forced degradation studies, for which fragments generated upon thermal stress were clearly identified, with no deconjugation of the drug linker observed for the T-GlyGLICK-DM1 ADC. Lastly, innovative ion mobility-based collision-induced unfolding (CIU) approaches were used to assess the gas-phase behavior of compounds along the conjugation process, highlighting an increased resistance of the mAb against gas-phase unfolding upon drug conjugation. Altogether, these state-of-the-art nMS methods represent innovative approaches to investigate drug loading and distribution of last generation ADCs, their evolution during the bioconjugation process and their impact on gas-phase stabilities. We envision nMS and CIU methods to improve the conformational characterization of next generation-empowered mAb-derived products such as engineered nanobodies, bispecific ADCs or immunocytokines.

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Newly developed instrumentation for measuring highly oxidized molecules at atmospheric pressure

10.5194/egusphere-egu21-12911 ◽

2021 ◽

Author(s):

Paap Koemets ◽

Sander Mirme ◽

Kuno Kooser ◽

Heikki Junninen

Keyword(s):

Gas Phase ◽

Atmospheric Chemistry ◽

Atmospheric Pressure ◽

Chemical Ionization ◽

Measurement Technology ◽

Differential Mobility Analyzer ◽

Neutral Cluster ◽

Differential Mobility ◽

Alpha Pinene ◽

Ambient Measurements

The Highly Oxidized Molecule Ion Spectrometer (HOMIS) is a novel instrument for measuring the total concentration of highly oxidized molecules (HOM-s) (Bianchi et al., 2019) at atmospheric pressure. The device combines a chemical ionization charger with a multi-channel differential mobility analyzer. The chemical ionization charger is based on the principles outlined by Eisele and Tanner (1993). The charger is attached to a parallel differential mobility analyzer identical to the ones used in the Neutral cluster and Air Ion Spectrometer (NAIS, Mirme 2011), but with modified sample and sheath air flow rates to improve the mobility resolution of the device. The complete mobility distribution in the range from 3.2 to 0.056 cm2/V/s is measured simultaneously by 25 electrometers. The range captures the charger ions, monomers, dimers, trimers but also extends far towards larger particles to possibly detect larger HOM-s that have not been measured with existing instrumentation. The maximum time resolution of the device is 1 second allowing it to detect rapid changes in the sample. The device has been designed to be easy to use, require little maintenance and work reliably in various environments during long term measurements.First results of the prototype were acquired from laboratory experiments and ambient measurements. Experiments were conducted at the Laboratory of Environmental Physics, University of Tartu. The sample was drawn from a reaction chamber where alpha-pinene and ozone were introduced. Initial results show a good response when concentrations of alpha-pinene and ozone were changed.&#160;Ambient measurements were conducted at the SMEAR Estonia measurement station in a hemiboreal forest for 10 days in the spring and two months in the winter of 2020. The HOMIS measurements were performed together with a CI-APi-TOF (Jokinen et al., 2012).&#160;References:Bianchi, F., Kurt&#233;n, T., Riva, M., Mohr, C., Rissanen, M. P., Roldin, P., Berndt, T., Crounse, J. D., Wennberg, P. O., Mentel, T. F., Wildt, J., Junninen, H., Jokinen, T., Kulmala, M., Worsnop, D. R., Thornton, J. A., Donahue, N., Kjaergaard, H. G. and Ehn, M. (2019), &#8220;Highly Oxygenated Organic Molecules (HOM) from Gas-Phase Autoxidation Involving Peroxy Radicals: A Key Contributor to Atmospheric Aerosol&#8221;, Chemical Reviews, 119, 6, 3472&#8211;3509Eisele, F. L., Tanner D. J. (1993), &#8220;Measurement of the gas phase concentration of H2SO4 and methane sulfonic acid and estimates of H2SO4 production and loss in the atmosphere&#8221;, JGR: Atmospheres, 98, 9001-9010Jokinen T., Sipil&#228; M., Junninen H., Ehn M., L&#246;nn G., Hakala J., Pet&#228;j&#228; T., Mauldin III R. L., Kulmala M., and Worsnop D. R. (2012), &#8220;Atmospheric sulphuric acid and neutral cluster measurements using CI-APi-TOF&#8221;, Atmospheric Chemistry and Physics, 12, 4117&#8211;4125Mirme, S. (2011), &#8220;Development of nanometer aerosol measurement technology&#8221;, Doctoral thesis, University of Tartu

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Formation of highly oxygenated organic molecules from chlorine-atom-initiated oxidation of alpha-pinene

Atmospheric Chemistry and Physics ◽

10.5194/acp-20-5145-2020 ◽

2020 ◽

Vol 20 (8) ◽

pp. 5145-5155 ◽

Cited By ~ 4

Author(s):

Yonghong Wang ◽

Matthieu Riva ◽

Hongbin Xie ◽

Liine Heikkinen ◽

Simon Schallhart ◽

...

Keyword(s):

Organic Molecules ◽

Organic Aerosol ◽

Heterogeneous Reactions ◽

Peroxy Radicals ◽

Chlorine Atoms ◽

Uncertainty Range ◽

Nitryl Chloride ◽

Alpha Pinene ◽

Calibration Methods ◽

Substantial Uncertainty

Abstract. Highly oxygenated organic molecules (HOMs) from atmospheric oxidation of alpha-pinene can irreversibly condense to particles and contribute to secondary organic aerosol (SOA) formation. Recently, the formation of nitryl chloride (ClNO2) from heterogeneous reactions, followed by its subsequent photolysis, is suggested to be an important source of chlorine atoms in many parts of the atmosphere. However, the oxidation of monoterpenes such as alpha-pinene by chlorine atoms has received very little attention, and the ability of this reaction to form HOMs is completely unstudied. Here, chamber experiments were conducted with alpha-pinene and chlorine under low- and high-nitrogen-oxide (NOx, NOx=NO+NO2) conditions. A nitrate-based CI-APi-ToF (chemical ionization–atmospheric pressure interface–time of flight) mass spectrometer was used to measure HOM products. Clear distributions of monomers with 9–10 carbon atoms and dimers with 18–20 carbon atoms were observed under low-NOx conditions. With increased concentration of NOx within the chamber, the formation of dimers was suppressed due to the reactions of peroxy radicals with NO. We estimated the HOM yields from chlorine-initiated oxidation of alpha-pinene under low-NOx conditions to be around 1.8 %, though with a substantial uncertainty range (0.8 %–4 %) due to lack of suitable calibration methods. Corresponding yields at high NOx could not be determined because of concurrent ozonolysis reactions. Our study demonstrates that also the oxidation of alpha-pinene by chlorine atoms and yield low-volatility organic compounds.

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