scholarly journals Technical Note: Development of chemoinformatic tools to enumerate functional groups in molecules for organic aerosol characterization

2016 ◽  
Vol 16 (7) ◽  
pp. 4401-4422 ◽  
Author(s):  
Giulia Ruggeri ◽  
Satoshi Takahama
Keyword(s):  
Functional Groups ◽  
Chemical Speciation ◽  
Organic Aerosol ◽  
Technical Note ◽  
Carbon Oxidation ◽  
Estimation Model ◽  
Aerosol Composition ◽  
Reduced Representation ◽  
Complete Set ◽  
Chamber Studies

Abstract. Functional groups (FGs) can be used as a reduced representation of organic aerosol composition in both ambient and controlled chamber studies, as they retain a certain chemical specificity. Furthermore, FG composition has been informative for source apportionment, and various models based on a group contribution framework have been developed to calculate physicochemical properties of organic compounds. In this work, we provide a set of validated chemoinformatic patterns that correspond to (1) a complete set of functional groups that can entirely describe the molecules comprised in the α-pinene and 1,3,5-trimethylbenzene MCMv3.2 oxidation schemes, (2) FGs that are measurable by Fourier transform infrared spectroscopy (FTIR), (3) groups incorporated in the SIMPOL.1 vapor pressure estimation model, and (4) bonds necessary for the calculation of carbon oxidation state. We also provide example applications for this set of patterns. We compare available aerosol composition reported by chemical speciation measurements and FTIR for different emission sources, and calculate the FG contribution to the O : C ratio of simulated gas-phase composition generated from α-pinene photooxidation (using the MCMv3.2 oxidation scheme).

scholarly journals Technical Note: Development of chemoinformatic tools to enumerate functional groups in molecules for organic aerosol characterization

2015 ◽  
Vol 15 (22) ◽  
pp. 33631-33674 ◽  
Author(s):  
G. Ruggeri ◽  
S. Takahama
Keyword(s):  
Functional Groups ◽  
Chemical Speciation ◽  
Organic Aerosol ◽  
Technical Note ◽  
Carbon Oxidation ◽  
Estimation Model ◽  
Aerosol Composition ◽  
Reduced Representation ◽  
Complete Set ◽  
Chamber Studies

Abstract. Functional groups (FGs) can be used as a reduced representation of organic aerosol composition in both ambient and environmental controlled chamber studies, as they retain a certain chemical specificity. Furthermore, FG composition has been informative for source apportionment, and various models based on a group contribution framework have been developed to calculate physicochemical properties of organic compounds. In this work, we provide a set of validated chemoinformatic patterns that correspond to: (1) groups incorporated in the SIMPOL.1 vapor pressure estimation model, (2) FGs that are measurable by Fourier transform infrared spectroscopy (FTIR), (3) a complete set of functional groups that can entirely describe the molecules comprised in the α-pinene and 1,3,5-trimethylbenzene MCMv3.2 oxidation schemes, and (4) bonds necessary for the calculation of carbon oxidation state. We also provide example applications for this set of patterns. We compare available aerosol composition reported by chemical speciation measurements and FTIR for different emission sources, and calculate the FG contribution to the O : C ratio of simulated gas phase composition generated from α-pinene photooxidation (using MCMv3.2 oxidation scheme).

scholarly journals Technical Note: Relating functional group measurements to carbon types for improved model-measurement comparisons of organic aerosol composition

2016 ◽  
Author(s):  
Satoshi Takahama ◽  
Giulia Ruggeri
Keyword(s):  
Organic Carbon ◽  
Functional Group ◽  
Organic Aerosol ◽  
Chem Phys ◽  
Technical Note ◽  
Molecular Structures ◽  
Organic Carbon Content ◽  
Aerosol Composition ◽  
Ft Ir ◽  
Model Measurement

Abstract. Functional group (FG) analysis provides a means by which functionalization in organic aerosol can be attributed to the abundances of its underlying molecular structures. However, performing this attribution requires additional, unobserved details about the molecular mixture to provide constraints in the estimation process. To address this issue, we present an approach for conceptualizing FG measurements of organic aerosol in terms of its functionalized carbon atoms. This reformulation facilitates estimation of mass recovery and biases in popular carbon-centric metrics that describe the extent of functionalization (such as oxygen to carbon ratio, organic mass to organic carbon mass ratio, and mean carbon oxidation state) for any given set of molecules and FGs analyzed. Furthermore, this approach allows development of parameterizations to more precisely estimate the organic carbon content from measured FG abundance. We use simulated photooxidation products of α-pinene secondary organic aerosol previously reported by Ruggeri et al. (Atmos. Chem. Phys., 16, 4401–4422, 2016) and FG measurements by Fourier Transform Infrared (FT-IR) spectroscopy in chamber experiments by Sax et al. (Aerosol Sci. Tech., 39, 822–830, 2005) to infer the relationships among molecular composition, FG composition, and metrics of organic aerosol functionalization. We find that for this simulated system, ~ 80 % of the carbon atoms should be detected by FGs for which calibration models are commonly developed, and ~ 7 % of the carbon atoms are undetectable by FT-IR analysis because they are not associated with vibrational modes in the infrared. Estimated biases due to undetected carbon fraction for these simulations are used to make adjustments in these carbon-centric metrics such that model-measurement differences are framed in terms of unmeasured heteroatoms (e.g., in hydroperoxide and nitrate groups for the case studied in this demonstration). The formality of this method provides framework for extending FG analysis to not only model-measurement but also instrument intercomparisons in other chemical systems.

scholarly journals Technical Note: Vapor pressure estimation methods applied to secondary organic aerosol constituents from α-pinene oxidation: an intercomparison study

2010 ◽  
Vol 10 (13) ◽  
pp. 6271-6282 ◽  
Author(s):  
S. Compernolle ◽  
K. Ceulemans ◽  
J.-F. Müller
Keyword(s):  
Vapor Pressure ◽  
Functional Groups ◽  
State Of The Art ◽  
Organic Aerosol ◽  
Technical Note ◽  
Estimation Methods ◽  
Vapor Pressures ◽  
Aerosol Formation ◽  
Pressure Estimation ◽  
Intercomparison Study

Abstract. We applied and compared seven vapor pressure estimation methods to the condensable compounds generated in the oxidation of α-pinene, as described by the state-of-the-art mechanism of the BOREAM model Capouet et al., 2008. Several of these methods had to be extended in order to treat functional groups such as hydroperoxides and peroxy acyl nitrates. Large differences in the estimated vapor pressures are reported, which will inevitably lead to large differences in aerosol formation simulations. Cautioning remarks are given for some vapor pressure estimation methods.

scholarly journals Technical note: Vapor pressure estimation methods applied to secondary organic aerosol constituents from α-pinene oxidation: an intercomparison study

2010 ◽  
Vol 10 (4) ◽  
pp. 8487-8513 ◽  
Author(s):  
S. Compernolle ◽  
K. Ceulemans ◽  
J.-F. Müller
Keyword(s):  
Vapor Pressure ◽  
Functional Groups ◽  
State Of The Art ◽  
Organic Aerosol ◽  
Technical Note ◽  
Estimation Methods ◽  
Vapor Pressures ◽  
Aerosol Formation ◽  
Pressure Estimation ◽  
Intercomparison Study

Abstract. We applied and compared seven vapor pressure estimation methods to the condensable compounds generated in the oxidation of α-pinene, as described by the state-of-the-art mechanism of the BOREAM model (Capouet et al., 2008). Several of these methods had to be extended in order to treat functional groups such as hydroperoxides and peroxy acyl nitrates. Large differences in the estimated vapor pressures are reported, which will inevitably lead to large differences in aerosol formation simulations. Cautioning remarks are given for some vapor pressure estimation methods.

scholarly journals Biogenic oxidized organic functional groups in aerosol particles from a mountain forest site and their similarities to laboratory chamber products

2010 ◽  
Vol 10 (2) ◽  
pp. 4789-4822 ◽  
Author(s):  
R. E. Schwartz ◽  
L. M. Russell ◽  
S. J. Sjosted ◽  
A. Vlasenko ◽  
J. G. Slowik ◽  
...  
Keyword(s):  
Carboxylic Acid ◽  
Functional Groups ◽  
Functional Group ◽  
Group Composition ◽  
Organic Aerosol ◽  
Anthropogenic Sources ◽  
Forest Site ◽  
Aerosol Composition ◽  
X Ray ◽  
Organic Functional Groups

Abstract. Submicron particles collected at Whistler, British Columbia, at 1020 masl during May and June 2008 on Teflon filters were analyzed by Fourier transform infrared (FTIR) and X-ray fluorescence (XRF) techniques for organic functional groups (OFG) and elemental composition. Organic mass (OM) ranged from less than 0.5 to 3.1μg m−3, with a project mean and standard deviation of 1.3±1.0 μg m−3 and 0.21±0.16 μg m−3 for OM and sulfate, respectively. On average, organic hydroxyl, alkane, and carboxylic acid groups represented 34%, 33%, and 23% of OM, respectively. Ketone, amine and organosulfate groups constituted 6%, 5%, and <1% of the average organic aerosol composition, respectively. Measurements of volatile organic compounds (VOC), including isoprene and monoterpenes from biogenic VOC (BVOC) emissions and their oxidation products (methyl-vinylketone/methacrolein, MVK/MACR), were made using co-located proton transfer reaction mass spectrometry (PTR-MS). We present chemically-specific evidence of OFG associated with BVOC emissions. Positive matrix factorization (PMF) analysis attributed 65% of the campaign OM to biogenic sources, based on the correlations of one factor to monoterpenes and MVK/MACR. The remaining fraction was attributed to anthropogenic sources based on a correlation to sulfate. The functional group composition of the biogenic factor (consisting of 32% alkane, 25% carboxylic acid, 2% organic hydroxyl, 16% ketone, and 6% amine groups) was similar to that of secondary organic aerosol (SOA) reported from the oxidation of BVOCs in laboratory chamber studies, providing evidence that the magnitude and chemical composition of biogenic SOA simulated in the laboratory is similar to that found in actual atmospheric conditions. The biogenic factor OM is also correlated to dust elements, indicating that dust may act as a non-acidic SOA sink. This role is supported by the organic functional group composition and morphology of single particles, which were analyzed by scanning transmission X-ray microscopy near edge X-ray absorption fine structure (STXM-NEXAFS).

scholarly journals Biogenic oxidized organic functional groups in aerosol particles from a mountain forest site and their similarities to laboratory chamber products

2010 ◽  
Vol 10 (11) ◽  
pp. 5075-5088 ◽  
Author(s):  
R. E. Schwartz ◽  
L. M. Russell ◽  
S. J. Sjostedt ◽  
A. Vlasenko ◽  
J. G. Slowik ◽  
...  
Keyword(s):  
Carboxylic Acid ◽  
Functional Groups ◽  
Functional Group ◽  
Group Composition ◽  
Organic Aerosol ◽  
Anthropogenic Sources ◽  
Forest Site ◽  
Aerosol Composition ◽  
X Ray ◽  
Organic Functional Groups

Abstract. Submicron particles collected at Whistler, British Columbia, at 1020 m a.s.l. during May and June 2008 on Teflon filters were analyzed by Fourier transform infrared (FTIR) and X-ray fluorescence (XRF) techniques for organic functional groups (OFG) and elemental composition. Organic mass (OM) concentrations ranged from less than 0.5 to 3.1 μg m−3, with a project mean and standard deviation of 1.3±1.0 μg m−3 and 0.21±0.16 μg m−3 for OM and sulfate, respectively. On average, organic hydroxyl, alkane, and carboxylic acid groups represented 34%, 33%, and 23% of OM, respectively. Ketone, amine and organosulfate groups constituted 6%, 5%, and <1% of the average organic aerosol composition, respectively. Measurements of volatile organic compounds (VOC), including isoprene and monoterpenes from biogenic VOC (BVOC) emissions and their oxidation products (methyl-vinylketone / methacrolein, MVK/MACR), were made using co-located proton transfer reaction mass spectrometry (PTR-MS). We present chemically-specific evidence of OFG associated with BVOC emissions. Positive matrix factorization (PMF) analysis attributed 65% of the campaign OM to biogenic sources, based on the correlations of one factor to monoterpenes and MVK/MACR. The remaining fraction was attributed to anthropogenic sources based on a correlation to sulfate. The functional group composition of the biogenic factor (consisting of 32% alkane, 25% carboxylic acid, 21% organic hydroxyl, 16% ketone, and 6% amine groups) was similar to that of secondary organic aerosol (SOA) reported from the oxidation of BVOCs in laboratory chamber studies, providing evidence that the magnitude and chemical composition of biogenic SOA simulated in the laboratory is similar to that found in actual atmospheric conditions. The biogenic factor OM is also correlated to dust elements, indicating that dust may act as a non-acidic SOA sink. This role is supported by the organic functional group composition and morphology of single particles, which were analyzed by scanning transmission X-ray microscopy near edge X-ray absorption fine structure (STXM-NEXAFS).

scholarly journals Technical note: Relating functional group measurements to carbon types for improved model–measurement comparisons of organic aerosol composition

2017 ◽  
Vol 17 (7) ◽  
pp. 4433-4450 ◽  
Author(s):  
Satoshi Takahama ◽  
Giulia Ruggeri
Keyword(s):  
Organic Carbon ◽  
Functional Group ◽  
Organic Aerosol ◽  
Technical Note ◽  
Molecular Structures ◽  
Organic Carbon Content ◽  
Aerosol Composition ◽  
Ft Ir ◽  
Improved Model ◽  
Model Measurement

Abstract. Functional group (FG) analysis provides a means by which functionalization in organic aerosol can be attributed to the abundances of its underlying molecular structures. However, performing this attribution requires additional, unobserved details about the molecular mixture to provide constraints in the estimation process. We present an approach for conceptualizing FG measurements of organic aerosol in terms of its functionalized carbon atoms. This reformulation facilitates estimation of mass recovery and biases in popular carbon-centric metrics that describe the extent of functionalization (such as oxygen to carbon ratio, organic mass to organic carbon mass ratio, and mean carbon oxidation state) for any given set of molecules and FGs analyzed. Furthermore, this approach allows development of parameterizations to more precisely estimate the organic carbon content from measured FG abundance. We use simulated photooxidation products of α-pinene secondary organic aerosol previously reported by Ruggeri et al. (2016) and FG measurements by Fourier transform infrared (FT-IR) spectroscopy in chamber experiments by Sax et al. (2005) to infer the relationships among molecular composition, FG composition, and metrics of organic aerosol functionalization. We find that for this simulated system, ∼ 80 % of the carbon atoms should be detected by FGs for which calibration models are commonly developed, and ∼ 7 % of the carbon atoms are undetectable by FT-IR analysis because they are not associated with vibrational modes in the infrared. Estimated biases due to undetected carbon fraction for these simulations are used to make adjustments in these carbon-centric metrics such that model–measurement differences are framed in terms of unmeasured heteroatoms (e.g., in hydroperoxide and nitrate groups for the case studied in this demonstration). The formality of this method provides framework for extending FG analysis to not only model–measurement but also instrument intercomparisons in other chemical systems.

scholarly journals Changes in organic aerosol composition with aging inferred from aerosol mass spectra

2011 ◽  
Vol 11 (13) ◽  
pp. 6465-6474 ◽  
Author(s):  
N. L. Ng ◽  
M. R. Canagaratna ◽  
J. L. Jimenez ◽  
P. S. Chhabra ◽  
J. H. Seinfeld ◽  
...  
Keyword(s):  
Chemical Composition ◽  
Organic Aerosols ◽  
Organic Aerosol ◽  
Aerosol Formation ◽  
Aerosol Composition ◽  
Bond Breakage ◽  
Aerosol Mass ◽  
Physical Mixing ◽  
Chamber Studies ◽  
Van Krevelen Diagram

Abstract. Organic aerosols (OA) can be separated with factor analysis of aerosol mass spectrometer (AMS) data into hydrocarbon-like OA (HOA) and oxygenated OA (OOA). We develop a new method to parameterize H:C of OOA in terms of f43 (ratio of m/z 43, mostly C2H3O+, to total signal in the component mass spectrum). Such parameterization allows for the transformation of large database of ambient OOA components from the f44 (mostly CO2+, likely from acid groups) vs. f43 space ("triangle plot") (Ng et al., 2010) into the Van Krevelen diagram (H:C vs. O:C) (Van Krevelen, 1950). Heald et al. (2010) examined the evolution of total OA in the Van Krevelen diagram. In this work total OA is deconvolved into components that correspond to primary (HOA and others) and secondary (OOA) organic aerosols. By deconvolving total OA into different components, we remove physical mixing effects between secondary and primary aerosols which allows for examination of the evolution of OOA components alone in the Van Krevelen space. This provides a unique means of following ambient secondary OA evolution that is analogous to and can be compared with trends observed in chamber studies of secondary organic aerosol formation. The triangle plot in Ng et al. (2010) indicates that f44 of OOA components increases with photochemical age, suggesting the importance of acid formation in OOA evolution. Once they are transformed with the new parameterization, the triangle plot of the OOA components from all sites occupy an area in Van Krevelen space which follows a ΔH:C/ΔO:C slope of ~ −0.5. This slope suggests that ambient OOA aging results in net changes in chemical composition that are equivalent to the addition of both acid and alcohol/peroxide functional groups without fragmentation (i.e. C-C bond breakage), and/or the addition of acid groups with fragmentation. These results provide a framework for linking the bulk aerosol chemical composition evolution to molecular-level studies.

scholarly journals Seasonal differences in oxygenated organic aerosol composition: implications for emissions sources and factor analysis

2015 ◽  
Vol 15 (12) ◽  
pp. 6993-7002 ◽  
Author(s):  
F. Canonaco ◽  
J. G. Slowik ◽  
U. Baltensperger ◽  
A. S. H. Prévôt
Keyword(s):  
Chemical Speciation ◽  
Organic Aerosol ◽  
Chemical Information ◽  
Organic Mass ◽  
Positive Matrix ◽  
Aerosol Composition ◽  
Aerosol Mass Spectrometer ◽  
Atmospheric Aging ◽  
Aerosol Mass ◽  
High Degree

Abstract. Aerosol chemical speciation monitor (ACSM) measurements were performed in Zurich, Switzerland, for 13 months (February 2011 through February 2012). Many previous studies using this or related instruments have utilized the fraction of organic mass measured at m/z 44 (f44), which is typically dominated by the CO2+ ion and related to oxygenation, as an indicator of atmospheric aging. The current study demonstrates that during summer afternoons, when photochemical processes are most vigorous as indicated by high oxidant – OX (O3 + NO2), f44 for ambient secondary organic aerosol (SOA) is not higher but is rather similar or lower than on days with low OX. On the other hand, f43 (less oxidized fragment) tends to increase. These changes are discussed in the f44 / f43 space frequently used to interpret ACSM and aerosol mass spectrometer (AMS) data. This is likely due to the formation of semi-volatile oxygenated aerosol produced from biogenic precursor gases, whose emissions increase with ambient temperature. In addition, source apportionment analyses conducted on winter and summer data using positive matrix factorization (PMF) yield semi-volatile oxygenated organic aerosol (SV-OOA) factors that retain source-related chemical information. Winter SV-OOA is highly influenced by biomass burning, whereas summer SV-OOA is to a high degree produced from biogenic precursor gases. These sources contribute to substantial differences between the winter and summer f44 / f43 data, suggesting that PMF analysis of multi-season data employing only two OOA factors cannot capture the seasonal variability of OOA.

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