commit f0354dd421e481cbc63685bae7b9fdbda0586545 Author: daviditschan Date: Mon Aug 31 10:01:18 2026 +0200 First commit: adding all .tex files to git. diff --git a/chapters/acknowledgements.ist b/chapters/acknowledgements.ist new file mode 100644 index 0000000..1120ab8 --- /dev/null +++ b/chapters/acknowledgements.ist @@ -0,0 +1,29 @@ +% makeindex style file created by the glossaries package +% for document 'acknowledgements' on 2026-8-11 +actual '?' +encap '|' +level '!' +quote '"' +keyword "\\glossaryentry" +preamble "\\glossarysection[\\glossarytoctitle]{\\glossarytitle}\\glossarypreamble\n\\begin{theglossary}\\glossaryheader\n" +postamble "\%\n\\end{theglossary}\\glossarypostamble\n" +group_skip "\\glsgroupskip\n" +item_0 "\%\n" +item_1 "\%\n" +item_2 "\%\n" +item_01 "\%\n" +item_x1 "\\relax \\glsresetentrylist\n" +item_12 "\%\n" +item_x2 "\\relax \\glsresetentrylist\n" +delim_0 "\{\\glossaryentrynumbers\{\\relax " +delim_1 "\{\\glossaryentrynumbers\{\\relax " +delim_2 "\{\\glossaryentrynumbers\{\\relax " +delim_t "\}\}" +delim_n "\\delimN " +delim_r "\\delimR " +headings_flag 1 +heading_prefix "\\glsgroupheading\{" +heading_suffix "\}\\relax \\glsresetentrylist " +symhead_positive "glssymbols" +numhead_positive "glsnumbers" +page_compositor "." diff --git a/chapters/acknowledgements.pdf b/chapters/acknowledgements.pdf new file mode 100644 index 0000000..d221322 Binary files /dev/null and b/chapters/acknowledgements.pdf differ diff --git a/chapters/acknowledgements.tex b/chapters/acknowledgements.tex new file mode 100644 index 0000000..edca3da --- /dev/null +++ b/chapters/acknowledgements.tex @@ -0,0 +1,22 @@ +% !TeX program = lualatex + +%% ------------------------------------------------------------------% +%% SUBFILE MODE +\documentclass[../main/main.tex]{subfiles} +\graphicspath{{../graphics/}} + + +%% ------------------------------------------------------------------% +%% DOCUMENT + + +\begin{document} + + \pagestyle{mainbody} + + \chapter{Acknowledgements} + \thispagestyle{mainbody} + + Dr. David Bell, Laso Blabla, Dominik Blabla, Wei Huang, Thorsten Bartels-Rausch, Marco Paolini, Yiwei Gong, Sacha Fallah, Francesca Salteri, + +\end{document} \ No newline at end of file diff --git a/chapters/conclusion.tex b/chapters/conclusion.tex new file mode 100644 index 0000000..ed2c5c2 --- /dev/null +++ b/chapters/conclusion.tex @@ -0,0 +1,85 @@ +% !TeX program = lualatex + +%% ------------------------------------------------------------------% +%% SUBFILE MODE +\documentclass[../main/main.tex]{subfiles} +\graphicspath{{../graphics/}} + + +%% ------------------------------------------------------------------% +%% DOCUMENT + + +\begin{document} + + \pagestyle{mainbody} + + \chapter{Introduction} + \thispagestyle{mainbody} + + + Iodine is the heaviest stable halogen element with atomic number \qty{53}{}. It has an average atomic weight of \qty{126.904}{\amu} and forms a semi-lustrous solid under standard conditions (here \qty{273.15}{\kelvin} and \qty{1}{\bar}, see \citet{calvert_glossary_1990}) \citep{kaiho_physical_2015}. Its melting and boiling points are \qty{114}{\degreeCelsius} and \qty{184}{\degreeCelsius}, respectively, and its vapour pressure is \qty{0.031}{\kilo\pascal} and \qty{9.17}{\kilo\pascal} at \qty{25}{\degreeCelsius} and \qty{113.6}{\degreeCelsius}, respectively \citep{kaiho_physical_2015}. The atomic radius of iodine is \qty{140}{\pico\meter} and its first ionisation energy is \qty{1015}{\kilo\joule\per\mol} \citep{kaiho_physical_2015}. Iodine is important in the enviornment: in the atmosphere, it influences the chemistry of ozone and important radical species, and it may be cause the formation of particles that may act as nuclei for aerosol or clouds \citep{saiz-lopez_atmospheric_2012}. The former is important for the capability of the atmophere to oxidise and remove species emitted to it, while the latter is important because of its effect on radiative equilibrium of Earth. + + \section{Iodine in the environment} + + Iodine is litophilic and incompatible in Earth's astenosphere, and therefore concentrated in oceans and surface sediments \citep{kendrick_halogen_2024}. Marine sediments constitute the largest iodine reservoir \citep{kendrick_halogen_2024} with much higher concentrations of \qtyrange{20}{600}{\milli\gram\per\kilogram} compared to soil- (\qtyrange{0.5}{20}{\milli\gram\per\kilogram}) or rock (\qtyrange{0.08}{0.5}{\milli\gram\per\kilogram}) concentrations \citep{whitehead_distribution_1984}. Sedimented iodine may be recycled into the oceans through sedimentary brines \citep{muramatsu_recycling_2001, muramatsu_studies_2004} around techtonically active subduction zones \citep{carrano_influence_2020} through diagenesis processes involving thermal decompostion or microbiological reduction of buried organic matter \citep{kendrick_halogen_2024, muramatsu_recycling_2001}. Consequently, iodine concentrations in the oceans are approximately \qtyrange{45}{60}{\micro\gram\per\liter} \citep{whitehead_distribution_1984}, mostly in the form of \gls{IO3-f}, the thermodynamically most stable state of iodine in aqueous solution \citep{fuge_iodine_2015}. However, \gls{IO3-f} exhibits a nutrient-like profile \citep{carrano_influence_2020} being depleted at the surface, whereas \gls{I-f} is enriched in the surface \citep{elderfield_biophilic_1980}. Similarly, organic matter is enriched in the surface, so that the existence of some iodinated organics may be presumed \citep{saiz-lopez_atmospheric_2012}. Within the oceans, iodine is incorporated preferrentially in organic matter \citep{kendrick_halogen_2024} by micro- and macroalgae, and aerobic bacteria \citep{carpenter_biogeochemical_2015}: through faciliated diffusion (see detailed descriptions in \citet{kupper_iodide_2008, winter_exploring_2009, amachi_microbial_2008}), cells store iodine as \ce{\glssymbol{I-f}(aq)} or associated to organic molecules \citep{kupper_iodide_2008, amachi_microbial_2008}. + \Gls{I-f} within the cell interior may act as an antioxidant \citep{kupper_iodide_2008}: upon oxidative stress, the \gls{I-f} reservoir is mobilised and cells emit \ce{\glssymbol{I-f}(aq)} and a range of \glspl{VOICa} \citep{kupper_iodide_2008, carpenter_biogeochemical_2015} that may volatilise to the atmosphere. Analogously, when oxidative stress occurs during air exposure at low tide, the hetergeneous surface reaction of \gls{I-f} and \gls{O3f} at the sea-water interface produces \gls{HOIf}, \gls{I2f} and \glspl{IO.f} directly emitted to the atmosphere \citep{carpenter_biogeochemical_2015, palmer_iodine_2005, liu_kinetics_2001, sakamoto_direct_2009, hayase_heterogeneous_2010, he_role_2021}. It is currently thought that the biggest source of inorganic iodine to the atmosphere is \gls{HOIf} produced via the same pathway, exceeding the emissions of \gls{I2f} by one order of magnitude \citep{carpenter_atmospheric_2013}. + Nevertheless, the atmospheric iodine budget is currently not well-constrained \citep{saiz-lopez_atmospheric_2012}. \glspl{VOICa} (notably \ce{\glssymbol{CH3If}}) and inorganic iodine species (\ce{\glssymbol{HOIf}}, \ce{\glssymbol{I2f}}, \ce{\glssymbol{IO.f}}) emitted from the oceans constitute the biggest source of iodine to the atmosphere \citep{carpenter_biogeochemical_2015, carpenter_atmospheric_2013}, with estimated input $\approx\qty{550}{\giga\gram\per\year}$ \citep{saiz-lopez_atmospheric_2012}. Most \glspl{VOICa} are photolabile with lifetimes on the order of minutes to days \citep{bloss_kinetics_2001}. Other natural sources of iodine to the amtosphere include soils and plants \citep{whitehead_distribution_1984, carpenter_biogeochemical_2015, fuge_iodine_2015}, terrestrial water systems \citep{whitehead_distribution_1984}, and volcanoes or salt lakes \citep{carpenter_biogeochemical_2015}. The additional input from terrestrial sources into the atmosphere is $\approx\qtyrange{80}{110}{\giga\gram\per\year}$ \citep{saiz-lopez_atmospheric_2012}. Anthropogenic sources include direct emissions from fossil fuel burning \citep{fuge_iodine_2015} and pesticide use \citep{zheng_accelerated_2003, whitehead_distribution_1984}. There are indirect anthropogenic effects as well: ice core data indicates that the sea-air flux of iodine has tripled between 1950 and 2010 as a consequence of increased anthropogenic ozone pollution of the troposphere \citep{cuevas_rapid_2018}. Sinks of atmospheric iodine include wet- and dry deposition \citep{fuge_iodine_2015}, and direct uptake through plants \citep{fuge_iodine_2015}. Overall, this leads to boundary layer mixing ratios of $\chi_{\ce{\glssymbol{I2f}(g)}}\leq\qty{93}{\pptv}$ \citep{carpenter_biogeochemical_2015}, $\chi_{\ce{\glssymbol{IO.f}(g)}}\leq\qtyrange{3}{20}{\pptv}$ \citep{carpenter_biogeochemical_2015}, $\chi_{\ce{\glssymbol{HOIf}(g)}}\leq\qty{1}{\pptv}$ \citep{he_role_2021} and $\chi_{\ce{\glssymbol{I.f}(g)}}\leq\qtyrange{0.1}{22}{\pptv}$ \citep{carpenter_biogeochemical_2015, he_role_2021}. + + \section{Iodine Chemistry in the Atmosphere} + + The importance of the marine iodine source is likely also reflected in aerosol composition: above marine areas, aerosol is enriched in iodine relative to seawater content by a factor of \qtyrange{100}{1000}{} \citep{carpenter_biogeochemical_2015}. Iodine may be transported into the aerosol phase through bubble-bursting of iodine-rich surface ocean waters \citep{saiz-lopez_atmospheric_2012}, or through the formation of aerosol via \glspl{IOPa} \citep{odowd_marine_2002}. Likely, low-volatility iodinated organics may also condense into the aerosol phase. Overall, various iodinated species may be present in aerosol including \gls{I-f}, \gls{IO3-f}, \gls{HOIf} and \gls{SOIa} \citep{saiz-lopez_atmospheric_2012}. \Citet{saiz-lopez_atmospheric_2012, gilfedder_iodine_2008} report that \gls{SOIa} is very frequent in aerosol and may constitute the largest reservoir of iodine in aerosol. There appear to be two principal pathways of \gls{SOIa} accomodation: direct accumulation from sea spray enriched in iodinated organics, and the reaction of \gls{HOIf} with aerosol organics. \Gls{HOIf} may also be highly reactive towards other species, likely due to its affinity for nucelophilic attacks on susceptible species. In general however, \gls{HOIf} or other likewise reduced iodine species such as \gls{I-f} should be oxidised to \gls{IO3-f} \citep{gilfedder_iodine_2008}, the thermodynamically most stable form of iodine in aqueous solution. Consequently, the accumulated form of iodine in condensed aerosol phases is often thought to be \gls{IO3-f} \citep{gilfedder_iodine_2008, saiz-lopez_atmospheric_2012}. However, observations in the troposphere indicate higher aerosol contents of \gls{I-f} than \gls{IO3-f} \citep{gilfedder_iodine_2008}, or high variability in the \gls{I-f}/\gls{IO3-f} ratio \citep{saiz-lopez_atmospheric_2012}. This indicates the presence of a mechanism reducing \gls{IO3-f} in the troposphere. + + Hetergeneous aerosol chemistry of iodine is closely linked to homogeneous chemistry of iodine through many iodine species. Generally, atmospheric iodine chemistry is initiated mostly through \gls{RISa} such as \glspl{I.f} or \glspl{IO.f}. Briefly, homogeneous iodine chemistry involves catalytic destruction of troposheric ozone via various pathways involving \glspl{HOxf} and \glspl{NOxf} as well as other halogen atoms in the atmosphere \citep{saiz-lopez_reactive_2012}. This process is photochemically driven and initiated with \glssymbol{IO.f} and \glssymbol{I.f}. \citet{saiz-lopez_reactive_2012} have outlined the mechanism: the intial step is the production of \glspl{I.f} from \glspl{RInf} or \gls{I2f}. The \glspl{I.f} react with \gls{O3f} to produce \glspl{IO.f} that in turn recombine to again produce \glspl{I.f}: + + \begin{reactions} + \RI{}(g) + ${h\nu}$ &-> R^{\bullet}(g) + \glssymbol{I.f}(g)\\ + \glssymbol{I2f}(g) + ${h\nu}$ &-> 2 \glssymbol{I.f}(g)\\ + \glssymbol{I.f}(g) + \glssymbol{O3f}(g) &-> \glssymbol{IO.f}(g) + \glssymbol{O2f}(g) \label{reac: intro: iodine radical ozone loss}\\ + 2\glssymbol{IO.f} &-> 2\glssymbol{I.f}(g) + \glssymbol{O2f}(g)\label{reac: intro: 2IO to 2I and O2} + \end{reactions} + The net outcome is ozone destruction with \ce{2\glssymbol{O3f}(g) -> 3\glssymbol{O2f}(g)}, although reaction \ref{reac: intro: 2IO to 2I and O2} has other channels that may involve \glssymbol{HOxf} and \glssymbol{NOxf} cycles. Importantly, the \gls{IO.f} has a lifetime against photolysis in the boundary layer on the order of seconds \citep{bloss_kinetics_2001}. Likewise, the effective lifetime of \gls{Ix.f} against uptake in aerosol is on the order of hours \citep{dix_detection_2013}: sustained presence of \glspl{IO.f} in the atmosphere therefore requires an effective recycling mechanism for \ce{\glssymbol{IO.f}}. + + Additionally, iodine may be involved in the oxidation of atmospheric organic molecules or mercury, allowing the latter to enter the food chain as highly poisonous methylmercury \citep{steffen_synthesis_2008, saiz-lopez_reactive_2012, saiz-lopez_atmospheric_2012}, and likely leading to enhanced condensation of organics into the aerosol phase through the former. Further, through formation of \glspl{IOPa}, iodine oxides may lead to the production of \glspl{UFAPa} \citep{carpenter_biogeochemical_2015}. Volatile species may condense on \glspl{UFAPa} that can grow up to the point of becoming \glspl{CCNa} \citep{saiz-lopez_atmospheric_2012}. Recent evidence shows that nucleation via iodine oxoacids to produce \glspl{IOPa} is highly efficient and sometimes competitive with sulfuric acid-ammonium driven nucleation \citep{he_role_2021}. Moreover, heterogeneous iodine chemistry on pre-existing frozen or liquid salt particles may lead to sudden increases in gas phase iodine species \citep{saiz-lopez_reactive_2012}. Importantly, the reaction of \gls{Br-f} with \gls{O3f} on frozen salt solutions occurs in the brine pertaining to the bulk ice phase, rather than \emph{within} the bulk ice phase \citep{oldridge_formation_2011}: such brines are formed when freezing solutions exclude solutes --- the heterogeneous reaction of \gls{O3f} with \gls{I-f} on frozen aerosol is here assumed to behave similarly. In other words, the heterogeneous reaction of \gls{O3f} with aerosol surfaces is assumed to be similar for frozen and liquid aerosol particles. + + Other heterogeneous effects may lead to substantial iodine emissions through the reaction of ozone with dissolved \gls{I-f} in ocean and aerosols \citep{palmer_iodine_2005, liu_kinetics_2001, sakamoto_direct_2009, hayase_heterogeneous_2010}. In the upper troposphere and lower stratosphere, heterogeneous recycling of iodine species is highly important: Model calculations by \citet{saiz-lopez_injection_2015} show that from the lower troposphere, convection may transport inorganic- and organic iodine species to the lower stratosphere, causing a \gls{Iyf} injection of \qtyrange{0.25}{0.7}{\pptv} \citep{saiz-lopez_injection_2015}. Measurements by \citet{koenig_quantitative_2020} are in agreement with this, indicating an injection of \qty{0.77\pm0.10}{\pptv} of \glssymbol{Iyf} into the lower stratosphere. Associated therewith is a mixing ratio of $\chi_{\ce{\glssymbol{IO.f}(g)}}=\qty{0.06\pm0.03}{\pptv}$ even for aged stratospheric air. \Citet{koenig_quantitative_2020} also observed that increases in altitude across the troposphere are associated with (1) an increase in particulate iodine and a decrease in gas phase iodine; and (2) a shift of \gls{I-f}-\gls{IO3-f} speciation in the condensed phase towards \gls{IO3-f}. Simulations could reproduce observed $\chi_{\ce{\glssymbol{IO.f}(g)}}$ only when a recycling scheme for iodine on ice particles was applied, and when the proper partioning between condensed- and gas phase was applied. This indicates that, as for the troposphere, a recycling mechanism producing gas phase \glspl{IO.f} must exist. There is also evidence that \gls{IO3-f} should be reduced to \gls{I-f}: \citet{pillar-little_conversion_2013} have established a pathway through which \gls{I-f} and \gls{O3f} cause volatilization of \ce{\glssymbol{I2f}(g)} and \ce{\glssymbol{HOIf}(g)} from watery microdroplets. However, it is still unclear \emph{how} the necessary \gls{I-f} is formed, given that most iodine should be present as \gls{IO3-f}. Consequently, an important question to answer is: how is \glssymbol{IO3-f} reduced to species --- most likely \glssymbol{I-f} --- that may, directly of after reacting, volatilise to the gas phase? + + \section{Reduction of Iodate} + + \Citet{saunders_insights_2012} have shown that \gls{IO3-f} may be reduced when solutions of \gls{IO3-f} and \gls{HAa} are irradiated with \gls{UV-Aa} and \gls{VISa} light between $\gls{LAMBDAs}\geq\qty{310}{\nano\meter}$ and $\gls{LAMBDAs}\approx\qty{780}{\nano\meter}$. The light source was filtered to exclude \gls{IRa} light and lamp output below $\gls{LAMBDAs}=\qty{310}{\nano\meter}$ to simulate the \gls{UV-Aa}-\gls{VISa} solar spectrum in the lower troposphere. They found that the major product of this photochemically induced process was \gls{SOIa} and that the proportion of \gls{I-f} in the reactant solution remained constant at approximately \qty{20}{\percent}. Since \gls{HAa} is a \gls{CHROMOPHOREg}, the suggested mechanism involves photogeneration of solvated electrons \ce{e-(aq)} that, in dependence of \gls{pHs}, yield \gls{HOIf}: \ce{\glssymbol{IO3-f}(aq) + 4e-(aq) + 5\glssymbol{H+f}(aq) ->\glssymbol{HOIf}(aq) + 2\glssymbol{H2Of}(aq)}. From there, \gls{SOIa} may be created through the nucleophilic attack of \gls{HOIf} on diphenolic functional groups \citep{saunders_insights_2012}. Alternatively, \gls{I2f} may be produced through reaction \ref{reac: intro: HOI to I2}, as described by \citet{pillar-little_conversion_2013}: + + \begin{reaction} + \glssymbol{HOIf}(aq) + \glssymbol{I-f} + \glssymbol{H+f}(aq) -> \glssymbol{I2f}(aq) + \glssymbol{H2Of}(l) \label{reac: intro: HOI to I2} + \end{reaction} + Since \gls{I2f} is insoluble \citep{saiz-lopez_atmospheric_2012}, there will be volatilisation of \gls{I2f} to the gas phase. Overall, the mechanism suggested by \citet{saunders_insights_2012} produces primarily \gls{HOIf} \gls{I2f} --- the production pathway of \gls{I-f} has not been elucidated. The presence of \gls{I-f}, however, appears necessary for the production of \ce{\glssymbol{I2f}(g)}. It is hypothetised that \gls{I-f} may be regenerated from \gls{SOIa} \citep{saunders_insights_2012, baker_marine_2005}. Finally, \citet{saunders_insights_2012} have reported oscillations in the release of \ce{\glssymbol{I2f}(g)}. This is likely associated with formation of \gls{H2O2f} as a byproduct of \gls{HAa} photolysis \citep{saunders_insights_2012}. Indeed, \citet{cooper_photochemical_1988} have shown that \gls{H2O2f} is a common product when irradiating aqueous solutions of \glspl{CHROMOPHOREg}. Given \gls{H2O2f}, oscillations in \ce{\glssymbol{I2f}}-\ce{\glssymbol{IO3-f}} are known as the \gls{BRAY-LIEBHAFSKY-MECHANISMa}, first described by \citet{bray_periodic_1921, bray_reactions_1931}: \gls{H2O2f} interacts with \gls{I2f} and \gls{IO3-f} via + + \begin{reactions} + &2\glssymbol{IO3-f}(aq) + 2\glssymbol{H+f}(aq) + 5\glssymbol{H2O2f}(aq) <=> \glssymbol{I2f}(aq) + 5\glssymbol{O2f}(g) + 6\glssymbol{H2Of}(l) \label{reac: oxidation of iodine through hydrogen peroxide}\\ + &\glssymbol{I2f}(aq) + 5\glssymbol{H2O2f}(aq) <=> 2\glssymbol{IO3-f}(aq) + 2\glssymbol{H+f}(aq) + 4\glssymbol{H2Of}(l) \label{reac: reduction of iodate through hydrogen peroxide} + \end{reactions} + to yield a net catalytic decomposition of \gls{H2O2f} via + + \begin{reaction} + 2\glssymbol{H2O2f}(aq) -> 2\glssymbol{H2Of}(l) + \glssymbol{O2f}(g) \label{reac: net catalytic destruction of hydrogen peroxide through iodine-iodate system} + \end{reaction} + The oscillation reaction has a \emph{stable} regime --- here, all species reach steady state except \glssymbol{H2O2f}: likely, \glssymbol{O2f}\ce{(g)} volatilises and \gls{LE-CHATELIER-PRINCIPLEa} dictates that \gls{H2O2f} consequently depletes. The \emph{unstable} regime where either reaction \ref{reac: oxidation of iodine through hydrogen peroxide} or \ref{reac: reduction of iodate through hydrogen peroxide} occur preferrentially, leads to oscillations in \gls{I2f} and \gls{IO3-f}. These oscillations are modulated by initial \gls{pHs} \citep{bray_periodic_1921} and temperature. Including an organic reducing agent and a metal-ion catalyst results in the \gls{BRIGGS-RAUSCHER-MECHANISMa} after \citet{briggs_oscillating_1973}, elucidated by \citet{schmitz_kinetics_2012}: Briefly, in addition to reaction \ref{reac: reduction of iodate through hydrogen peroxide}, the presence of some organic species \ce{R-H2} will induce the following reactions: + + \begin{reactions} + \glssymbol{H+f}(aq) + \glssymbol{IO3-f}(aq) + 2\glssymbol{I2f}(aq) + 5 R-H2(aq) &-> 5 R-HI + 3\glssymbol{H2Of}\\ + \glssymbol{H+f}(aq) + \glssymbol{IO3-f}(aq) + 2\glssymbol{I2f}(aq) + 5 R-HI(aq) &-> 5 R-I2 + 3\glssymbol{H2Of}\\ + R-I2 + R-H2 &<=> 2 R-HI + \end{reactions} + The backward reaction likely proceeds via the metal ion catalyst, although \citet{schmitz_kinetics_2012} reported the possibility of non-catalysed pathways. + + A lot has been learned so far: organic substances may lead to the reduction of \gls{IO3-f}, via \gls{CHROMOPHOREg} activity. Furthermore, observed oscillations in gas phase \ce{\glssymbol{I2f}} may be explained through \gls{BRAY-LIEBHAFSKY-MECHANISMa}-\gls{BRIGGS-RAUSCHER-MECHANISMa} mechanisms. However, the suitability of \glspl{HAa} to represent organic aerosol has been questioned: \citet{graber_atmospheric_2006} suggested that humic-like substances found in aerosol particles may differ substantially from humic substances found in soil. More specifically, \citet{graber_atmospheric_2006} argue that terrestrial sources --- from which the \gls{HAa} used by \citet{saunders_insights_2012} likely originate --- may not be the origin of the majority of humic-like substances in aerosol. Differences may be found in terms of molecular weight, aromatic moiety content, surface properties and other properties \citep{graber_atmospheric_2006}. Although \glspl{HAa} as organics have profen useful to elucidate the mechanisms of \glssymbol{I2f} recycling, quantitatively constraining this recycling better requires more realistic organics. Another important question to answer, therefore, is: are there proxies that represent organics in aerosol more accurately, and to which the same \gls{CHROMOPHOREg}-dependent pathway of iodine recycling applies? + + \section{Reduction of Iodate: Proxies for Secondary Organic Aerosol} + + \Citet{guenther_global_1995} modelled global natural \gls{VOCa} emissions in 1990. They found a total flux of $\qty{1150}{\tera\gramCarbon\per\year}$, of which \qty{44}{\percent} (\qty{503}{\tera\gramCarbon\per\year}) was \gls{ISOPRENEf} and \qty{11}{\percent} (\qty{127}{\tera\gramCarbon\per\year}) were monoterpenes such as \gls{A-PINENEf}. Thereof, approximately \qty{75}{\percent} orginated from forests. In 2006, The annual atmospheric \gls{VOCa} injection was further specified in 2012 when \citet{guenther_model_2012} reported the following emissions of \glspl{VOCa} for the year 2000: total emissions were \qty{1089}{\tera\gramCarbon\per\year}, of which \gls{ISOPRENEf} emissions were \qty{49.1}{\percent} (\qty{535}{\tera\gramCarbon\per\year}) and the monoterpenes \gls{A-PINENEf}, \gls{B-PINENEf} and \gls{LIMONENEf} contributed \qty{6.7}{\percent} (\qty{66.1}{\tera\gramCarbon\per\year}), \qty{1.7}{\percent} (\qty{18.9}{\tera\gramCarbon\per\year}) and \qty{1.0}{\percent} (\qty{11.4}{\tera\gramCarbon\per\year}), respectively. \gls{ISOPRENEf} and monoterpene emissions are biogenic and mostly linked to vegetation --- overall they contributed approximately \qty{65}{\percent} to global \gls{VOCa} emissions in 2000 \citep{guenther_model_2012}, rendering them a major source of atmospheric \glspl{VOCa}. + + Organic matter in aerosol is present either as \gls{POAa} or \gls{SOAa}. \gls{POAa} and \gls{SOAa} comprise the largest share of \emph{fine} particles with diameters $d\leq\qty{2.5}{\micro\meter}$. On the other hand, large particles with diameters $d>\qty{2.5}{\micro\meter}$ are mostly comprised of particles formed mechanically, including soil and mineral dust, sea salt particles and plant particles \citep{jziemann_kinetics_2012}. \gls{POAa} requires no chemical reactions to condense to the aerosol phase. Conversely, \gls{SOAa} is created when volatile precursor species are chemically altered to lower volatilities, and consequently condense to the aerosol phase. Likely, \gls{SOAa} constitues a large fraction of organic aerosol \cite{bianchi_highly_2019, hallquist_formation_2009}. As a general rule of thumb, higher oxygen content of a molecule indicates \emph{lower} volatility. Therefore, oxidation reactions are highly important in \gls{SOAa} formation because oxidation effectively \emph{decreases} volatility. Recent work summarised by \citet{bianchi_highly_2019} suggests that there exists class of of low-volatile species referred to as \glspl{HOMa} with low volatility. Such \glspl{HOMa} are formed through \emph{autooxidation} reactions involving peroxy radicals: this process is detailed by \citet{bianchi_highly_2019}, and the subtle but important difference between \glspl{HOMa} and molecules with high oxygen content is laid out. Briefly, \glspl{HOMa} are species of very low vapour pressure so that condensation onto existing particles is very probable and almost irreversible \citep{bianchi_highly_2019}. High yields of \glspl{HOMa} have been observed for \gls{ISOPRENEf} and the monoterpenes \gls{A-PINENEf} and especially \gls{LIMONENEf} \citep{bianchi_highly_2019}, with total yields of \qty{4}{\percent} (\gls{ISOPRENEf}), \qtyrange{7.0\pm3.5}{3.4\pm1.0}{\percent} (\gls{A-PINENEf}) and \qty{17.0\pm8.5}{\percent} (\gls{LIMONENEf}), respectively \citep{bianchi_highly_2019, jokinen_production_2015, ng_secondary_2008, ehn_large_2014, kirkby_ion-induced_2016}. It may therefore be assumed that derivatives --- or more precisely oxidation products --- of monoterpenes or \gls{ISOPRENEf} are common in \gls{SOAa}. Building on the work of \citet{saunders_insights_2012}, chosing an oxidation product of \gls{ISOPRENEf} or monoterpenes as the investigated organics may constitute a more realistc proxy for aerosol organics. + + Recently, \citet{reza_iodine_2024} have performed similar experiments as \citet{saunders_insights_2012}, but using organic species better representing \gls{VOCa} oxidation. Recent observations have shown elevated concentrations of \ce{\glssymbol{IO.f}(g)} in dust layers above the Atacama and Sechura deserts: \citet{koenig_ozone_2021} measured a ten-fold enhancement of \gls{IO.f} concentrations compared to the regional background signal of \qtyrange{0.10}{0.25}{\pptv}. Because iron is hypothetised to catalyse photochemistry in dust particles, and since it is the most abundant transition metal in dust minerals \citep{aal-abadleh_perspective_2023}, iron may serve as a proxy for dust when investigating the reduction of \gls{IO3-f}. In a series of \gls{CWFTRa} experiments, \citet{reza_iodine_2024} used a \gls{CE-DOASa} to detect \glssymbol{I2f}\ce{(g)} and a \gls{ToF I-CIMSa} to detect \glspl{OVOCa} associated with \gls{IO3-f} reduction in thin aqueous films. The films were inserted into the \gls{CWFTRa} and consisted of an organic or inorganic matrix and \gls{IO3-f}. + The organic matrices included \gls{IRON-3-CITRATEa}, \gls{CAa} and \gls{BTCAa}. \gls{CAa} was found in aerosol \citep{lienhard_measurements_2012} and is a proxy for oxygenated organic species. \gls{IRON-3-CITRATEa}, as a known photoactive compound, is considered a suitable proxy for \ce{Fe}(\toRoman{3}) carboxylate complexes found in the atmosphere \citep{reza_iodine_2024}. Importantly, \gls{CAa} has well-characterised hygroscopic properties \citep{reza_iodine_2024} so that this matrix can be used to control against \glspl{MATRIX-EFFECT-(CHEM)g} of organics that are due to iron when using \gls{IRON-3-CITRATEa}. These matrices were mixed with a solution of \gls{NaIO3f} to introduce \gls{IO3-f} at a concentration of $\approx\qty{30}{\milli\Molar}$. The results show that irradiation with \gls{VISa} for films containing \gls{IRON-3-CITRATEa} led to the reduction of $\approx\qty{40}{\percent}$ of the initially present \gls{IO3-f}. Likely, \gls{IRON-3-CITRATEa} undergoes a \gls{LMCTa} induced through irradiance with a photon at $\lambda<\qty{500}{\nano\meter}$ to yield \gls{CITRATEa} radicals and solvated electrons \ce{e-(aq)}, as described by \citet{saunders_insights_2012}. Likely, reduction of \gls{IO3-f} is driven through these solvated electrons. Furthermore, \citet{reza_iodine_2024} report that the speciation of the \glspl{CHROMOPHOREg} may include iodine-containing compounds. + +\end{document} \ No newline at end of file diff --git a/chapters/discussion.tex b/chapters/discussion.tex new file mode 100644 index 0000000..ed2c5c2 --- /dev/null +++ b/chapters/discussion.tex @@ -0,0 +1,85 @@ +% !TeX program = lualatex + +%% ------------------------------------------------------------------% +%% SUBFILE MODE +\documentclass[../main/main.tex]{subfiles} +\graphicspath{{../graphics/}} + + +%% ------------------------------------------------------------------% +%% DOCUMENT + + +\begin{document} + + \pagestyle{mainbody} + + \chapter{Introduction} + \thispagestyle{mainbody} + + + Iodine is the heaviest stable halogen element with atomic number \qty{53}{}. It has an average atomic weight of \qty{126.904}{\amu} and forms a semi-lustrous solid under standard conditions (here \qty{273.15}{\kelvin} and \qty{1}{\bar}, see \citet{calvert_glossary_1990}) \citep{kaiho_physical_2015}. Its melting and boiling points are \qty{114}{\degreeCelsius} and \qty{184}{\degreeCelsius}, respectively, and its vapour pressure is \qty{0.031}{\kilo\pascal} and \qty{9.17}{\kilo\pascal} at \qty{25}{\degreeCelsius} and \qty{113.6}{\degreeCelsius}, respectively \citep{kaiho_physical_2015}. The atomic radius of iodine is \qty{140}{\pico\meter} and its first ionisation energy is \qty{1015}{\kilo\joule\per\mol} \citep{kaiho_physical_2015}. Iodine is important in the enviornment: in the atmosphere, it influences the chemistry of ozone and important radical species, and it may be cause the formation of particles that may act as nuclei for aerosol or clouds \citep{saiz-lopez_atmospheric_2012}. The former is important for the capability of the atmophere to oxidise and remove species emitted to it, while the latter is important because of its effect on radiative equilibrium of Earth. + + \section{Iodine in the environment} + + Iodine is litophilic and incompatible in Earth's astenosphere, and therefore concentrated in oceans and surface sediments \citep{kendrick_halogen_2024}. Marine sediments constitute the largest iodine reservoir \citep{kendrick_halogen_2024} with much higher concentrations of \qtyrange{20}{600}{\milli\gram\per\kilogram} compared to soil- (\qtyrange{0.5}{20}{\milli\gram\per\kilogram}) or rock (\qtyrange{0.08}{0.5}{\milli\gram\per\kilogram}) concentrations \citep{whitehead_distribution_1984}. Sedimented iodine may be recycled into the oceans through sedimentary brines \citep{muramatsu_recycling_2001, muramatsu_studies_2004} around techtonically active subduction zones \citep{carrano_influence_2020} through diagenesis processes involving thermal decompostion or microbiological reduction of buried organic matter \citep{kendrick_halogen_2024, muramatsu_recycling_2001}. Consequently, iodine concentrations in the oceans are approximately \qtyrange{45}{60}{\micro\gram\per\liter} \citep{whitehead_distribution_1984}, mostly in the form of \gls{IO3-f}, the thermodynamically most stable state of iodine in aqueous solution \citep{fuge_iodine_2015}. However, \gls{IO3-f} exhibits a nutrient-like profile \citep{carrano_influence_2020} being depleted at the surface, whereas \gls{I-f} is enriched in the surface \citep{elderfield_biophilic_1980}. Similarly, organic matter is enriched in the surface, so that the existence of some iodinated organics may be presumed \citep{saiz-lopez_atmospheric_2012}. Within the oceans, iodine is incorporated preferrentially in organic matter \citep{kendrick_halogen_2024} by micro- and macroalgae, and aerobic bacteria \citep{carpenter_biogeochemical_2015}: through faciliated diffusion (see detailed descriptions in \citet{kupper_iodide_2008, winter_exploring_2009, amachi_microbial_2008}), cells store iodine as \ce{\glssymbol{I-f}(aq)} or associated to organic molecules \citep{kupper_iodide_2008, amachi_microbial_2008}. + \Gls{I-f} within the cell interior may act as an antioxidant \citep{kupper_iodide_2008}: upon oxidative stress, the \gls{I-f} reservoir is mobilised and cells emit \ce{\glssymbol{I-f}(aq)} and a range of \glspl{VOICa} \citep{kupper_iodide_2008, carpenter_biogeochemical_2015} that may volatilise to the atmosphere. Analogously, when oxidative stress occurs during air exposure at low tide, the hetergeneous surface reaction of \gls{I-f} and \gls{O3f} at the sea-water interface produces \gls{HOIf}, \gls{I2f} and \glspl{IO.f} directly emitted to the atmosphere \citep{carpenter_biogeochemical_2015, palmer_iodine_2005, liu_kinetics_2001, sakamoto_direct_2009, hayase_heterogeneous_2010, he_role_2021}. It is currently thought that the biggest source of inorganic iodine to the atmosphere is \gls{HOIf} produced via the same pathway, exceeding the emissions of \gls{I2f} by one order of magnitude \citep{carpenter_atmospheric_2013}. + Nevertheless, the atmospheric iodine budget is currently not well-constrained \citep{saiz-lopez_atmospheric_2012}. \glspl{VOICa} (notably \ce{\glssymbol{CH3If}}) and inorganic iodine species (\ce{\glssymbol{HOIf}}, \ce{\glssymbol{I2f}}, \ce{\glssymbol{IO.f}}) emitted from the oceans constitute the biggest source of iodine to the atmosphere \citep{carpenter_biogeochemical_2015, carpenter_atmospheric_2013}, with estimated input $\approx\qty{550}{\giga\gram\per\year}$ \citep{saiz-lopez_atmospheric_2012}. Most \glspl{VOICa} are photolabile with lifetimes on the order of minutes to days \citep{bloss_kinetics_2001}. Other natural sources of iodine to the amtosphere include soils and plants \citep{whitehead_distribution_1984, carpenter_biogeochemical_2015, fuge_iodine_2015}, terrestrial water systems \citep{whitehead_distribution_1984}, and volcanoes or salt lakes \citep{carpenter_biogeochemical_2015}. The additional input from terrestrial sources into the atmosphere is $\approx\qtyrange{80}{110}{\giga\gram\per\year}$ \citep{saiz-lopez_atmospheric_2012}. Anthropogenic sources include direct emissions from fossil fuel burning \citep{fuge_iodine_2015} and pesticide use \citep{zheng_accelerated_2003, whitehead_distribution_1984}. There are indirect anthropogenic effects as well: ice core data indicates that the sea-air flux of iodine has tripled between 1950 and 2010 as a consequence of increased anthropogenic ozone pollution of the troposphere \citep{cuevas_rapid_2018}. Sinks of atmospheric iodine include wet- and dry deposition \citep{fuge_iodine_2015}, and direct uptake through plants \citep{fuge_iodine_2015}. Overall, this leads to boundary layer mixing ratios of $\chi_{\ce{\glssymbol{I2f}(g)}}\leq\qty{93}{\pptv}$ \citep{carpenter_biogeochemical_2015}, $\chi_{\ce{\glssymbol{IO.f}(g)}}\leq\qtyrange{3}{20}{\pptv}$ \citep{carpenter_biogeochemical_2015}, $\chi_{\ce{\glssymbol{HOIf}(g)}}\leq\qty{1}{\pptv}$ \citep{he_role_2021} and $\chi_{\ce{\glssymbol{I.f}(g)}}\leq\qtyrange{0.1}{22}{\pptv}$ \citep{carpenter_biogeochemical_2015, he_role_2021}. + + \section{Iodine Chemistry in the Atmosphere} + + The importance of the marine iodine source is likely also reflected in aerosol composition: above marine areas, aerosol is enriched in iodine relative to seawater content by a factor of \qtyrange{100}{1000}{} \citep{carpenter_biogeochemical_2015}. Iodine may be transported into the aerosol phase through bubble-bursting of iodine-rich surface ocean waters \citep{saiz-lopez_atmospheric_2012}, or through the formation of aerosol via \glspl{IOPa} \citep{odowd_marine_2002}. Likely, low-volatility iodinated organics may also condense into the aerosol phase. Overall, various iodinated species may be present in aerosol including \gls{I-f}, \gls{IO3-f}, \gls{HOIf} and \gls{SOIa} \citep{saiz-lopez_atmospheric_2012}. \Citet{saiz-lopez_atmospheric_2012, gilfedder_iodine_2008} report that \gls{SOIa} is very frequent in aerosol and may constitute the largest reservoir of iodine in aerosol. There appear to be two principal pathways of \gls{SOIa} accomodation: direct accumulation from sea spray enriched in iodinated organics, and the reaction of \gls{HOIf} with aerosol organics. \Gls{HOIf} may also be highly reactive towards other species, likely due to its affinity for nucelophilic attacks on susceptible species. In general however, \gls{HOIf} or other likewise reduced iodine species such as \gls{I-f} should be oxidised to \gls{IO3-f} \citep{gilfedder_iodine_2008}, the thermodynamically most stable form of iodine in aqueous solution. Consequently, the accumulated form of iodine in condensed aerosol phases is often thought to be \gls{IO3-f} \citep{gilfedder_iodine_2008, saiz-lopez_atmospheric_2012}. However, observations in the troposphere indicate higher aerosol contents of \gls{I-f} than \gls{IO3-f} \citep{gilfedder_iodine_2008}, or high variability in the \gls{I-f}/\gls{IO3-f} ratio \citep{saiz-lopez_atmospheric_2012}. This indicates the presence of a mechanism reducing \gls{IO3-f} in the troposphere. + + Hetergeneous aerosol chemistry of iodine is closely linked to homogeneous chemistry of iodine through many iodine species. Generally, atmospheric iodine chemistry is initiated mostly through \gls{RISa} such as \glspl{I.f} or \glspl{IO.f}. Briefly, homogeneous iodine chemistry involves catalytic destruction of troposheric ozone via various pathways involving \glspl{HOxf} and \glspl{NOxf} as well as other halogen atoms in the atmosphere \citep{saiz-lopez_reactive_2012}. This process is photochemically driven and initiated with \glssymbol{IO.f} and \glssymbol{I.f}. \citet{saiz-lopez_reactive_2012} have outlined the mechanism: the intial step is the production of \glspl{I.f} from \glspl{RInf} or \gls{I2f}. The \glspl{I.f} react with \gls{O3f} to produce \glspl{IO.f} that in turn recombine to again produce \glspl{I.f}: + + \begin{reactions} + \RI{}(g) + ${h\nu}$ &-> R^{\bullet}(g) + \glssymbol{I.f}(g)\\ + \glssymbol{I2f}(g) + ${h\nu}$ &-> 2 \glssymbol{I.f}(g)\\ + \glssymbol{I.f}(g) + \glssymbol{O3f}(g) &-> \glssymbol{IO.f}(g) + \glssymbol{O2f}(g) \label{reac: intro: iodine radical ozone loss}\\ + 2\glssymbol{IO.f} &-> 2\glssymbol{I.f}(g) + \glssymbol{O2f}(g)\label{reac: intro: 2IO to 2I and O2} + \end{reactions} + The net outcome is ozone destruction with \ce{2\glssymbol{O3f}(g) -> 3\glssymbol{O2f}(g)}, although reaction \ref{reac: intro: 2IO to 2I and O2} has other channels that may involve \glssymbol{HOxf} and \glssymbol{NOxf} cycles. Importantly, the \gls{IO.f} has a lifetime against photolysis in the boundary layer on the order of seconds \citep{bloss_kinetics_2001}. Likewise, the effective lifetime of \gls{Ix.f} against uptake in aerosol is on the order of hours \citep{dix_detection_2013}: sustained presence of \glspl{IO.f} in the atmosphere therefore requires an effective recycling mechanism for \ce{\glssymbol{IO.f}}. + + Additionally, iodine may be involved in the oxidation of atmospheric organic molecules or mercury, allowing the latter to enter the food chain as highly poisonous methylmercury \citep{steffen_synthesis_2008, saiz-lopez_reactive_2012, saiz-lopez_atmospheric_2012}, and likely leading to enhanced condensation of organics into the aerosol phase through the former. Further, through formation of \glspl{IOPa}, iodine oxides may lead to the production of \glspl{UFAPa} \citep{carpenter_biogeochemical_2015}. Volatile species may condense on \glspl{UFAPa} that can grow up to the point of becoming \glspl{CCNa} \citep{saiz-lopez_atmospheric_2012}. Recent evidence shows that nucleation via iodine oxoacids to produce \glspl{IOPa} is highly efficient and sometimes competitive with sulfuric acid-ammonium driven nucleation \citep{he_role_2021}. Moreover, heterogeneous iodine chemistry on pre-existing frozen or liquid salt particles may lead to sudden increases in gas phase iodine species \citep{saiz-lopez_reactive_2012}. Importantly, the reaction of \gls{Br-f} with \gls{O3f} on frozen salt solutions occurs in the brine pertaining to the bulk ice phase, rather than \emph{within} the bulk ice phase \citep{oldridge_formation_2011}: such brines are formed when freezing solutions exclude solutes --- the heterogeneous reaction of \gls{O3f} with \gls{I-f} on frozen aerosol is here assumed to behave similarly. In other words, the heterogeneous reaction of \gls{O3f} with aerosol surfaces is assumed to be similar for frozen and liquid aerosol particles. + + Other heterogeneous effects may lead to substantial iodine emissions through the reaction of ozone with dissolved \gls{I-f} in ocean and aerosols \citep{palmer_iodine_2005, liu_kinetics_2001, sakamoto_direct_2009, hayase_heterogeneous_2010}. In the upper troposphere and lower stratosphere, heterogeneous recycling of iodine species is highly important: Model calculations by \citet{saiz-lopez_injection_2015} show that from the lower troposphere, convection may transport inorganic- and organic iodine species to the lower stratosphere, causing a \gls{Iyf} injection of \qtyrange{0.25}{0.7}{\pptv} \citep{saiz-lopez_injection_2015}. Measurements by \citet{koenig_quantitative_2020} are in agreement with this, indicating an injection of \qty{0.77\pm0.10}{\pptv} of \glssymbol{Iyf} into the lower stratosphere. Associated therewith is a mixing ratio of $\chi_{\ce{\glssymbol{IO.f}(g)}}=\qty{0.06\pm0.03}{\pptv}$ even for aged stratospheric air. \Citet{koenig_quantitative_2020} also observed that increases in altitude across the troposphere are associated with (1) an increase in particulate iodine and a decrease in gas phase iodine; and (2) a shift of \gls{I-f}-\gls{IO3-f} speciation in the condensed phase towards \gls{IO3-f}. Simulations could reproduce observed $\chi_{\ce{\glssymbol{IO.f}(g)}}$ only when a recycling scheme for iodine on ice particles was applied, and when the proper partioning between condensed- and gas phase was applied. This indicates that, as for the troposphere, a recycling mechanism producing gas phase \glspl{IO.f} must exist. There is also evidence that \gls{IO3-f} should be reduced to \gls{I-f}: \citet{pillar-little_conversion_2013} have established a pathway through which \gls{I-f} and \gls{O3f} cause volatilization of \ce{\glssymbol{I2f}(g)} and \ce{\glssymbol{HOIf}(g)} from watery microdroplets. However, it is still unclear \emph{how} the necessary \gls{I-f} is formed, given that most iodine should be present as \gls{IO3-f}. Consequently, an important question to answer is: how is \glssymbol{IO3-f} reduced to species --- most likely \glssymbol{I-f} --- that may, directly of after reacting, volatilise to the gas phase? + + \section{Reduction of Iodate} + + \Citet{saunders_insights_2012} have shown that \gls{IO3-f} may be reduced when solutions of \gls{IO3-f} and \gls{HAa} are irradiated with \gls{UV-Aa} and \gls{VISa} light between $\gls{LAMBDAs}\geq\qty{310}{\nano\meter}$ and $\gls{LAMBDAs}\approx\qty{780}{\nano\meter}$. The light source was filtered to exclude \gls{IRa} light and lamp output below $\gls{LAMBDAs}=\qty{310}{\nano\meter}$ to simulate the \gls{UV-Aa}-\gls{VISa} solar spectrum in the lower troposphere. They found that the major product of this photochemically induced process was \gls{SOIa} and that the proportion of \gls{I-f} in the reactant solution remained constant at approximately \qty{20}{\percent}. Since \gls{HAa} is a \gls{CHROMOPHOREg}, the suggested mechanism involves photogeneration of solvated electrons \ce{e-(aq)} that, in dependence of \gls{pHs}, yield \gls{HOIf}: \ce{\glssymbol{IO3-f}(aq) + 4e-(aq) + 5\glssymbol{H+f}(aq) ->\glssymbol{HOIf}(aq) + 2\glssymbol{H2Of}(aq)}. From there, \gls{SOIa} may be created through the nucleophilic attack of \gls{HOIf} on diphenolic functional groups \citep{saunders_insights_2012}. Alternatively, \gls{I2f} may be produced through reaction \ref{reac: intro: HOI to I2}, as described by \citet{pillar-little_conversion_2013}: + + \begin{reaction} + \glssymbol{HOIf}(aq) + \glssymbol{I-f} + \glssymbol{H+f}(aq) -> \glssymbol{I2f}(aq) + \glssymbol{H2Of}(l) \label{reac: intro: HOI to I2} + \end{reaction} + Since \gls{I2f} is insoluble \citep{saiz-lopez_atmospheric_2012}, there will be volatilisation of \gls{I2f} to the gas phase. Overall, the mechanism suggested by \citet{saunders_insights_2012} produces primarily \gls{HOIf} \gls{I2f} --- the production pathway of \gls{I-f} has not been elucidated. The presence of \gls{I-f}, however, appears necessary for the production of \ce{\glssymbol{I2f}(g)}. It is hypothetised that \gls{I-f} may be regenerated from \gls{SOIa} \citep{saunders_insights_2012, baker_marine_2005}. Finally, \citet{saunders_insights_2012} have reported oscillations in the release of \ce{\glssymbol{I2f}(g)}. This is likely associated with formation of \gls{H2O2f} as a byproduct of \gls{HAa} photolysis \citep{saunders_insights_2012}. Indeed, \citet{cooper_photochemical_1988} have shown that \gls{H2O2f} is a common product when irradiating aqueous solutions of \glspl{CHROMOPHOREg}. Given \gls{H2O2f}, oscillations in \ce{\glssymbol{I2f}}-\ce{\glssymbol{IO3-f}} are known as the \gls{BRAY-LIEBHAFSKY-MECHANISMa}, first described by \citet{bray_periodic_1921, bray_reactions_1931}: \gls{H2O2f} interacts with \gls{I2f} and \gls{IO3-f} via + + \begin{reactions} + &2\glssymbol{IO3-f}(aq) + 2\glssymbol{H+f}(aq) + 5\glssymbol{H2O2f}(aq) <=> \glssymbol{I2f}(aq) + 5\glssymbol{O2f}(g) + 6\glssymbol{H2Of}(l) \label{reac: oxidation of iodine through hydrogen peroxide}\\ + &\glssymbol{I2f}(aq) + 5\glssymbol{H2O2f}(aq) <=> 2\glssymbol{IO3-f}(aq) + 2\glssymbol{H+f}(aq) + 4\glssymbol{H2Of}(l) \label{reac: reduction of iodate through hydrogen peroxide} + \end{reactions} + to yield a net catalytic decomposition of \gls{H2O2f} via + + \begin{reaction} + 2\glssymbol{H2O2f}(aq) -> 2\glssymbol{H2Of}(l) + \glssymbol{O2f}(g) \label{reac: net catalytic destruction of hydrogen peroxide through iodine-iodate system} + \end{reaction} + The oscillation reaction has a \emph{stable} regime --- here, all species reach steady state except \glssymbol{H2O2f}: likely, \glssymbol{O2f}\ce{(g)} volatilises and \gls{LE-CHATELIER-PRINCIPLEa} dictates that \gls{H2O2f} consequently depletes. The \emph{unstable} regime where either reaction \ref{reac: oxidation of iodine through hydrogen peroxide} or \ref{reac: reduction of iodate through hydrogen peroxide} occur preferrentially, leads to oscillations in \gls{I2f} and \gls{IO3-f}. These oscillations are modulated by initial \gls{pHs} \citep{bray_periodic_1921} and temperature. Including an organic reducing agent and a metal-ion catalyst results in the \gls{BRIGGS-RAUSCHER-MECHANISMa} after \citet{briggs_oscillating_1973}, elucidated by \citet{schmitz_kinetics_2012}: Briefly, in addition to reaction \ref{reac: reduction of iodate through hydrogen peroxide}, the presence of some organic species \ce{R-H2} will induce the following reactions: + + \begin{reactions} + \glssymbol{H+f}(aq) + \glssymbol{IO3-f}(aq) + 2\glssymbol{I2f}(aq) + 5 R-H2(aq) &-> 5 R-HI + 3\glssymbol{H2Of}\\ + \glssymbol{H+f}(aq) + \glssymbol{IO3-f}(aq) + 2\glssymbol{I2f}(aq) + 5 R-HI(aq) &-> 5 R-I2 + 3\glssymbol{H2Of}\\ + R-I2 + R-H2 &<=> 2 R-HI + \end{reactions} + The backward reaction likely proceeds via the metal ion catalyst, although \citet{schmitz_kinetics_2012} reported the possibility of non-catalysed pathways. + + A lot has been learned so far: organic substances may lead to the reduction of \gls{IO3-f}, via \gls{CHROMOPHOREg} activity. Furthermore, observed oscillations in gas phase \ce{\glssymbol{I2f}} may be explained through \gls{BRAY-LIEBHAFSKY-MECHANISMa}-\gls{BRIGGS-RAUSCHER-MECHANISMa} mechanisms. However, the suitability of \glspl{HAa} to represent organic aerosol has been questioned: \citet{graber_atmospheric_2006} suggested that humic-like substances found in aerosol particles may differ substantially from humic substances found in soil. More specifically, \citet{graber_atmospheric_2006} argue that terrestrial sources --- from which the \gls{HAa} used by \citet{saunders_insights_2012} likely originate --- may not be the origin of the majority of humic-like substances in aerosol. Differences may be found in terms of molecular weight, aromatic moiety content, surface properties and other properties \citep{graber_atmospheric_2006}. Although \glspl{HAa} as organics have profen useful to elucidate the mechanisms of \glssymbol{I2f} recycling, quantitatively constraining this recycling better requires more realistic organics. Another important question to answer, therefore, is: are there proxies that represent organics in aerosol more accurately, and to which the same \gls{CHROMOPHOREg}-dependent pathway of iodine recycling applies? + + \section{Reduction of Iodate: Proxies for Secondary Organic Aerosol} + + \Citet{guenther_global_1995} modelled global natural \gls{VOCa} emissions in 1990. They found a total flux of $\qty{1150}{\tera\gramCarbon\per\year}$, of which \qty{44}{\percent} (\qty{503}{\tera\gramCarbon\per\year}) was \gls{ISOPRENEf} and \qty{11}{\percent} (\qty{127}{\tera\gramCarbon\per\year}) were monoterpenes such as \gls{A-PINENEf}. Thereof, approximately \qty{75}{\percent} orginated from forests. In 2006, The annual atmospheric \gls{VOCa} injection was further specified in 2012 when \citet{guenther_model_2012} reported the following emissions of \glspl{VOCa} for the year 2000: total emissions were \qty{1089}{\tera\gramCarbon\per\year}, of which \gls{ISOPRENEf} emissions were \qty{49.1}{\percent} (\qty{535}{\tera\gramCarbon\per\year}) and the monoterpenes \gls{A-PINENEf}, \gls{B-PINENEf} and \gls{LIMONENEf} contributed \qty{6.7}{\percent} (\qty{66.1}{\tera\gramCarbon\per\year}), \qty{1.7}{\percent} (\qty{18.9}{\tera\gramCarbon\per\year}) and \qty{1.0}{\percent} (\qty{11.4}{\tera\gramCarbon\per\year}), respectively. \gls{ISOPRENEf} and monoterpene emissions are biogenic and mostly linked to vegetation --- overall they contributed approximately \qty{65}{\percent} to global \gls{VOCa} emissions in 2000 \citep{guenther_model_2012}, rendering them a major source of atmospheric \glspl{VOCa}. + + Organic matter in aerosol is present either as \gls{POAa} or \gls{SOAa}. \gls{POAa} and \gls{SOAa} comprise the largest share of \emph{fine} particles with diameters $d\leq\qty{2.5}{\micro\meter}$. On the other hand, large particles with diameters $d>\qty{2.5}{\micro\meter}$ are mostly comprised of particles formed mechanically, including soil and mineral dust, sea salt particles and plant particles \citep{jziemann_kinetics_2012}. \gls{POAa} requires no chemical reactions to condense to the aerosol phase. Conversely, \gls{SOAa} is created when volatile precursor species are chemically altered to lower volatilities, and consequently condense to the aerosol phase. Likely, \gls{SOAa} constitues a large fraction of organic aerosol \cite{bianchi_highly_2019, hallquist_formation_2009}. As a general rule of thumb, higher oxygen content of a molecule indicates \emph{lower} volatility. Therefore, oxidation reactions are highly important in \gls{SOAa} formation because oxidation effectively \emph{decreases} volatility. Recent work summarised by \citet{bianchi_highly_2019} suggests that there exists class of of low-volatile species referred to as \glspl{HOMa} with low volatility. Such \glspl{HOMa} are formed through \emph{autooxidation} reactions involving peroxy radicals: this process is detailed by \citet{bianchi_highly_2019}, and the subtle but important difference between \glspl{HOMa} and molecules with high oxygen content is laid out. Briefly, \glspl{HOMa} are species of very low vapour pressure so that condensation onto existing particles is very probable and almost irreversible \citep{bianchi_highly_2019}. High yields of \glspl{HOMa} have been observed for \gls{ISOPRENEf} and the monoterpenes \gls{A-PINENEf} and especially \gls{LIMONENEf} \citep{bianchi_highly_2019}, with total yields of \qty{4}{\percent} (\gls{ISOPRENEf}), \qtyrange{7.0\pm3.5}{3.4\pm1.0}{\percent} (\gls{A-PINENEf}) and \qty{17.0\pm8.5}{\percent} (\gls{LIMONENEf}), respectively \citep{bianchi_highly_2019, jokinen_production_2015, ng_secondary_2008, ehn_large_2014, kirkby_ion-induced_2016}. It may therefore be assumed that derivatives --- or more precisely oxidation products --- of monoterpenes or \gls{ISOPRENEf} are common in \gls{SOAa}. Building on the work of \citet{saunders_insights_2012}, chosing an oxidation product of \gls{ISOPRENEf} or monoterpenes as the investigated organics may constitute a more realistc proxy for aerosol organics. + + Recently, \citet{reza_iodine_2024} have performed similar experiments as \citet{saunders_insights_2012}, but using organic species better representing \gls{VOCa} oxidation. Recent observations have shown elevated concentrations of \ce{\glssymbol{IO.f}(g)} in dust layers above the Atacama and Sechura deserts: \citet{koenig_ozone_2021} measured a ten-fold enhancement of \gls{IO.f} concentrations compared to the regional background signal of \qtyrange{0.10}{0.25}{\pptv}. Because iron is hypothetised to catalyse photochemistry in dust particles, and since it is the most abundant transition metal in dust minerals \citep{aal-abadleh_perspective_2023}, iron may serve as a proxy for dust when investigating the reduction of \gls{IO3-f}. In a series of \gls{CWFTRa} experiments, \citet{reza_iodine_2024} used a \gls{CE-DOASa} to detect \glssymbol{I2f}\ce{(g)} and a \gls{ToF I-CIMSa} to detect \glspl{OVOCa} associated with \gls{IO3-f} reduction in thin aqueous films. The films were inserted into the \gls{CWFTRa} and consisted of an organic or inorganic matrix and \gls{IO3-f}. + The organic matrices included \gls{IRON-3-CITRATEa}, \gls{CAa} and \gls{BTCAa}. \gls{CAa} was found in aerosol \citep{lienhard_measurements_2012} and is a proxy for oxygenated organic species. \gls{IRON-3-CITRATEa}, as a known photoactive compound, is considered a suitable proxy for \ce{Fe}(\toRoman{3}) carboxylate complexes found in the atmosphere \citep{reza_iodine_2024}. Importantly, \gls{CAa} has well-characterised hygroscopic properties \citep{reza_iodine_2024} so that this matrix can be used to control against \glspl{MATRIX-EFFECT-(CHEM)g} of organics that are due to iron when using \gls{IRON-3-CITRATEa}. These matrices were mixed with a solution of \gls{NaIO3f} to introduce \gls{IO3-f} at a concentration of $\approx\qty{30}{\milli\Molar}$. The results show that irradiation with \gls{VISa} for films containing \gls{IRON-3-CITRATEa} led to the reduction of $\approx\qty{40}{\percent}$ of the initially present \gls{IO3-f}. Likely, \gls{IRON-3-CITRATEa} undergoes a \gls{LMCTa} induced through irradiance with a photon at $\lambda<\qty{500}{\nano\meter}$ to yield \gls{CITRATEa} radicals and solvated electrons \ce{e-(aq)}, as described by \citet{saunders_insights_2012}. Likely, reduction of \gls{IO3-f} is driven through these solvated electrons. Furthermore, \citet{reza_iodine_2024} report that the speciation of the \glspl{CHROMOPHOREg} may include iodine-containing compounds. + +\end{document} \ No newline at end of file diff --git a/chapters/introduction.ist b/chapters/introduction.ist new file mode 100644 index 0000000..367c17a --- /dev/null +++ b/chapters/introduction.ist @@ -0,0 +1,29 @@ +% makeindex style file created by the glossaries package +% for document 'introduction' on 2026-5-26 +actual '?' +encap '|' +level '!' +quote '"' +keyword "\\glossaryentry" +preamble "\\glossarysection[\\glossarytoctitle]{\\glossarytitle}\\glossarypreamble\n\\begin{theglossary}\\glossaryheader\n" +postamble "\%\n\\end{theglossary}\\glossarypostamble\n" +group_skip "\\glsgroupskip\n" +item_0 "\%\n" +item_1 "\%\n" +item_2 "\%\n" +item_01 "\%\n" +item_x1 "\\relax \\glsresetentrylist\n" +item_12 "\%\n" +item_x2 "\\relax \\glsresetentrylist\n" +delim_0 "\{\\glossaryentrynumbers\{\\relax " +delim_1 "\{\\glossaryentrynumbers\{\\relax " +delim_2 "\{\\glossaryentrynumbers\{\\relax " +delim_t "\}\}" +delim_n "\\delimN " +delim_r "\\delimR " +headings_flag 1 +heading_prefix "\\glsgroupheading\{" +heading_suffix "\}\\relax \\glsresetentrylist " +symhead_positive "glssymbols" +numhead_positive "glsnumbers" +page_compositor "." diff --git a/chapters/introduction.pdf b/chapters/introduction.pdf new file mode 100644 index 0000000..1319a08 Binary files /dev/null and b/chapters/introduction.pdf differ diff --git a/chapters/introduction.tex b/chapters/introduction.tex new file mode 100644 index 0000000..ed2c5c2 --- /dev/null +++ b/chapters/introduction.tex @@ -0,0 +1,85 @@ +% !TeX program = lualatex + +%% ------------------------------------------------------------------% +%% SUBFILE MODE +\documentclass[../main/main.tex]{subfiles} +\graphicspath{{../graphics/}} + + +%% ------------------------------------------------------------------% +%% DOCUMENT + + +\begin{document} + + \pagestyle{mainbody} + + \chapter{Introduction} + \thispagestyle{mainbody} + + + Iodine is the heaviest stable halogen element with atomic number \qty{53}{}. It has an average atomic weight of \qty{126.904}{\amu} and forms a semi-lustrous solid under standard conditions (here \qty{273.15}{\kelvin} and \qty{1}{\bar}, see \citet{calvert_glossary_1990}) \citep{kaiho_physical_2015}. Its melting and boiling points are \qty{114}{\degreeCelsius} and \qty{184}{\degreeCelsius}, respectively, and its vapour pressure is \qty{0.031}{\kilo\pascal} and \qty{9.17}{\kilo\pascal} at \qty{25}{\degreeCelsius} and \qty{113.6}{\degreeCelsius}, respectively \citep{kaiho_physical_2015}. The atomic radius of iodine is \qty{140}{\pico\meter} and its first ionisation energy is \qty{1015}{\kilo\joule\per\mol} \citep{kaiho_physical_2015}. Iodine is important in the enviornment: in the atmosphere, it influences the chemistry of ozone and important radical species, and it may be cause the formation of particles that may act as nuclei for aerosol or clouds \citep{saiz-lopez_atmospheric_2012}. The former is important for the capability of the atmophere to oxidise and remove species emitted to it, while the latter is important because of its effect on radiative equilibrium of Earth. + + \section{Iodine in the environment} + + Iodine is litophilic and incompatible in Earth's astenosphere, and therefore concentrated in oceans and surface sediments \citep{kendrick_halogen_2024}. Marine sediments constitute the largest iodine reservoir \citep{kendrick_halogen_2024} with much higher concentrations of \qtyrange{20}{600}{\milli\gram\per\kilogram} compared to soil- (\qtyrange{0.5}{20}{\milli\gram\per\kilogram}) or rock (\qtyrange{0.08}{0.5}{\milli\gram\per\kilogram}) concentrations \citep{whitehead_distribution_1984}. Sedimented iodine may be recycled into the oceans through sedimentary brines \citep{muramatsu_recycling_2001, muramatsu_studies_2004} around techtonically active subduction zones \citep{carrano_influence_2020} through diagenesis processes involving thermal decompostion or microbiological reduction of buried organic matter \citep{kendrick_halogen_2024, muramatsu_recycling_2001}. Consequently, iodine concentrations in the oceans are approximately \qtyrange{45}{60}{\micro\gram\per\liter} \citep{whitehead_distribution_1984}, mostly in the form of \gls{IO3-f}, the thermodynamically most stable state of iodine in aqueous solution \citep{fuge_iodine_2015}. However, \gls{IO3-f} exhibits a nutrient-like profile \citep{carrano_influence_2020} being depleted at the surface, whereas \gls{I-f} is enriched in the surface \citep{elderfield_biophilic_1980}. Similarly, organic matter is enriched in the surface, so that the existence of some iodinated organics may be presumed \citep{saiz-lopez_atmospheric_2012}. Within the oceans, iodine is incorporated preferrentially in organic matter \citep{kendrick_halogen_2024} by micro- and macroalgae, and aerobic bacteria \citep{carpenter_biogeochemical_2015}: through faciliated diffusion (see detailed descriptions in \citet{kupper_iodide_2008, winter_exploring_2009, amachi_microbial_2008}), cells store iodine as \ce{\glssymbol{I-f}(aq)} or associated to organic molecules \citep{kupper_iodide_2008, amachi_microbial_2008}. + \Gls{I-f} within the cell interior may act as an antioxidant \citep{kupper_iodide_2008}: upon oxidative stress, the \gls{I-f} reservoir is mobilised and cells emit \ce{\glssymbol{I-f}(aq)} and a range of \glspl{VOICa} \citep{kupper_iodide_2008, carpenter_biogeochemical_2015} that may volatilise to the atmosphere. Analogously, when oxidative stress occurs during air exposure at low tide, the hetergeneous surface reaction of \gls{I-f} and \gls{O3f} at the sea-water interface produces \gls{HOIf}, \gls{I2f} and \glspl{IO.f} directly emitted to the atmosphere \citep{carpenter_biogeochemical_2015, palmer_iodine_2005, liu_kinetics_2001, sakamoto_direct_2009, hayase_heterogeneous_2010, he_role_2021}. It is currently thought that the biggest source of inorganic iodine to the atmosphere is \gls{HOIf} produced via the same pathway, exceeding the emissions of \gls{I2f} by one order of magnitude \citep{carpenter_atmospheric_2013}. + Nevertheless, the atmospheric iodine budget is currently not well-constrained \citep{saiz-lopez_atmospheric_2012}. \glspl{VOICa} (notably \ce{\glssymbol{CH3If}}) and inorganic iodine species (\ce{\glssymbol{HOIf}}, \ce{\glssymbol{I2f}}, \ce{\glssymbol{IO.f}}) emitted from the oceans constitute the biggest source of iodine to the atmosphere \citep{carpenter_biogeochemical_2015, carpenter_atmospheric_2013}, with estimated input $\approx\qty{550}{\giga\gram\per\year}$ \citep{saiz-lopez_atmospheric_2012}. Most \glspl{VOICa} are photolabile with lifetimes on the order of minutes to days \citep{bloss_kinetics_2001}. Other natural sources of iodine to the amtosphere include soils and plants \citep{whitehead_distribution_1984, carpenter_biogeochemical_2015, fuge_iodine_2015}, terrestrial water systems \citep{whitehead_distribution_1984}, and volcanoes or salt lakes \citep{carpenter_biogeochemical_2015}. The additional input from terrestrial sources into the atmosphere is $\approx\qtyrange{80}{110}{\giga\gram\per\year}$ \citep{saiz-lopez_atmospheric_2012}. Anthropogenic sources include direct emissions from fossil fuel burning \citep{fuge_iodine_2015} and pesticide use \citep{zheng_accelerated_2003, whitehead_distribution_1984}. There are indirect anthropogenic effects as well: ice core data indicates that the sea-air flux of iodine has tripled between 1950 and 2010 as a consequence of increased anthropogenic ozone pollution of the troposphere \citep{cuevas_rapid_2018}. Sinks of atmospheric iodine include wet- and dry deposition \citep{fuge_iodine_2015}, and direct uptake through plants \citep{fuge_iodine_2015}. Overall, this leads to boundary layer mixing ratios of $\chi_{\ce{\glssymbol{I2f}(g)}}\leq\qty{93}{\pptv}$ \citep{carpenter_biogeochemical_2015}, $\chi_{\ce{\glssymbol{IO.f}(g)}}\leq\qtyrange{3}{20}{\pptv}$ \citep{carpenter_biogeochemical_2015}, $\chi_{\ce{\glssymbol{HOIf}(g)}}\leq\qty{1}{\pptv}$ \citep{he_role_2021} and $\chi_{\ce{\glssymbol{I.f}(g)}}\leq\qtyrange{0.1}{22}{\pptv}$ \citep{carpenter_biogeochemical_2015, he_role_2021}. + + \section{Iodine Chemistry in the Atmosphere} + + The importance of the marine iodine source is likely also reflected in aerosol composition: above marine areas, aerosol is enriched in iodine relative to seawater content by a factor of \qtyrange{100}{1000}{} \citep{carpenter_biogeochemical_2015}. Iodine may be transported into the aerosol phase through bubble-bursting of iodine-rich surface ocean waters \citep{saiz-lopez_atmospheric_2012}, or through the formation of aerosol via \glspl{IOPa} \citep{odowd_marine_2002}. Likely, low-volatility iodinated organics may also condense into the aerosol phase. Overall, various iodinated species may be present in aerosol including \gls{I-f}, \gls{IO3-f}, \gls{HOIf} and \gls{SOIa} \citep{saiz-lopez_atmospheric_2012}. \Citet{saiz-lopez_atmospheric_2012, gilfedder_iodine_2008} report that \gls{SOIa} is very frequent in aerosol and may constitute the largest reservoir of iodine in aerosol. There appear to be two principal pathways of \gls{SOIa} accomodation: direct accumulation from sea spray enriched in iodinated organics, and the reaction of \gls{HOIf} with aerosol organics. \Gls{HOIf} may also be highly reactive towards other species, likely due to its affinity for nucelophilic attacks on susceptible species. In general however, \gls{HOIf} or other likewise reduced iodine species such as \gls{I-f} should be oxidised to \gls{IO3-f} \citep{gilfedder_iodine_2008}, the thermodynamically most stable form of iodine in aqueous solution. Consequently, the accumulated form of iodine in condensed aerosol phases is often thought to be \gls{IO3-f} \citep{gilfedder_iodine_2008, saiz-lopez_atmospheric_2012}. However, observations in the troposphere indicate higher aerosol contents of \gls{I-f} than \gls{IO3-f} \citep{gilfedder_iodine_2008}, or high variability in the \gls{I-f}/\gls{IO3-f} ratio \citep{saiz-lopez_atmospheric_2012}. This indicates the presence of a mechanism reducing \gls{IO3-f} in the troposphere. + + Hetergeneous aerosol chemistry of iodine is closely linked to homogeneous chemistry of iodine through many iodine species. Generally, atmospheric iodine chemistry is initiated mostly through \gls{RISa} such as \glspl{I.f} or \glspl{IO.f}. Briefly, homogeneous iodine chemistry involves catalytic destruction of troposheric ozone via various pathways involving \glspl{HOxf} and \glspl{NOxf} as well as other halogen atoms in the atmosphere \citep{saiz-lopez_reactive_2012}. This process is photochemically driven and initiated with \glssymbol{IO.f} and \glssymbol{I.f}. \citet{saiz-lopez_reactive_2012} have outlined the mechanism: the intial step is the production of \glspl{I.f} from \glspl{RInf} or \gls{I2f}. The \glspl{I.f} react with \gls{O3f} to produce \glspl{IO.f} that in turn recombine to again produce \glspl{I.f}: + + \begin{reactions} + \RI{}(g) + ${h\nu}$ &-> R^{\bullet}(g) + \glssymbol{I.f}(g)\\ + \glssymbol{I2f}(g) + ${h\nu}$ &-> 2 \glssymbol{I.f}(g)\\ + \glssymbol{I.f}(g) + \glssymbol{O3f}(g) &-> \glssymbol{IO.f}(g) + \glssymbol{O2f}(g) \label{reac: intro: iodine radical ozone loss}\\ + 2\glssymbol{IO.f} &-> 2\glssymbol{I.f}(g) + \glssymbol{O2f}(g)\label{reac: intro: 2IO to 2I and O2} + \end{reactions} + The net outcome is ozone destruction with \ce{2\glssymbol{O3f}(g) -> 3\glssymbol{O2f}(g)}, although reaction \ref{reac: intro: 2IO to 2I and O2} has other channels that may involve \glssymbol{HOxf} and \glssymbol{NOxf} cycles. Importantly, the \gls{IO.f} has a lifetime against photolysis in the boundary layer on the order of seconds \citep{bloss_kinetics_2001}. Likewise, the effective lifetime of \gls{Ix.f} against uptake in aerosol is on the order of hours \citep{dix_detection_2013}: sustained presence of \glspl{IO.f} in the atmosphere therefore requires an effective recycling mechanism for \ce{\glssymbol{IO.f}}. + + Additionally, iodine may be involved in the oxidation of atmospheric organic molecules or mercury, allowing the latter to enter the food chain as highly poisonous methylmercury \citep{steffen_synthesis_2008, saiz-lopez_reactive_2012, saiz-lopez_atmospheric_2012}, and likely leading to enhanced condensation of organics into the aerosol phase through the former. Further, through formation of \glspl{IOPa}, iodine oxides may lead to the production of \glspl{UFAPa} \citep{carpenter_biogeochemical_2015}. Volatile species may condense on \glspl{UFAPa} that can grow up to the point of becoming \glspl{CCNa} \citep{saiz-lopez_atmospheric_2012}. Recent evidence shows that nucleation via iodine oxoacids to produce \glspl{IOPa} is highly efficient and sometimes competitive with sulfuric acid-ammonium driven nucleation \citep{he_role_2021}. Moreover, heterogeneous iodine chemistry on pre-existing frozen or liquid salt particles may lead to sudden increases in gas phase iodine species \citep{saiz-lopez_reactive_2012}. Importantly, the reaction of \gls{Br-f} with \gls{O3f} on frozen salt solutions occurs in the brine pertaining to the bulk ice phase, rather than \emph{within} the bulk ice phase \citep{oldridge_formation_2011}: such brines are formed when freezing solutions exclude solutes --- the heterogeneous reaction of \gls{O3f} with \gls{I-f} on frozen aerosol is here assumed to behave similarly. In other words, the heterogeneous reaction of \gls{O3f} with aerosol surfaces is assumed to be similar for frozen and liquid aerosol particles. + + Other heterogeneous effects may lead to substantial iodine emissions through the reaction of ozone with dissolved \gls{I-f} in ocean and aerosols \citep{palmer_iodine_2005, liu_kinetics_2001, sakamoto_direct_2009, hayase_heterogeneous_2010}. In the upper troposphere and lower stratosphere, heterogeneous recycling of iodine species is highly important: Model calculations by \citet{saiz-lopez_injection_2015} show that from the lower troposphere, convection may transport inorganic- and organic iodine species to the lower stratosphere, causing a \gls{Iyf} injection of \qtyrange{0.25}{0.7}{\pptv} \citep{saiz-lopez_injection_2015}. Measurements by \citet{koenig_quantitative_2020} are in agreement with this, indicating an injection of \qty{0.77\pm0.10}{\pptv} of \glssymbol{Iyf} into the lower stratosphere. Associated therewith is a mixing ratio of $\chi_{\ce{\glssymbol{IO.f}(g)}}=\qty{0.06\pm0.03}{\pptv}$ even for aged stratospheric air. \Citet{koenig_quantitative_2020} also observed that increases in altitude across the troposphere are associated with (1) an increase in particulate iodine and a decrease in gas phase iodine; and (2) a shift of \gls{I-f}-\gls{IO3-f} speciation in the condensed phase towards \gls{IO3-f}. Simulations could reproduce observed $\chi_{\ce{\glssymbol{IO.f}(g)}}$ only when a recycling scheme for iodine on ice particles was applied, and when the proper partioning between condensed- and gas phase was applied. This indicates that, as for the troposphere, a recycling mechanism producing gas phase \glspl{IO.f} must exist. There is also evidence that \gls{IO3-f} should be reduced to \gls{I-f}: \citet{pillar-little_conversion_2013} have established a pathway through which \gls{I-f} and \gls{O3f} cause volatilization of \ce{\glssymbol{I2f}(g)} and \ce{\glssymbol{HOIf}(g)} from watery microdroplets. However, it is still unclear \emph{how} the necessary \gls{I-f} is formed, given that most iodine should be present as \gls{IO3-f}. Consequently, an important question to answer is: how is \glssymbol{IO3-f} reduced to species --- most likely \glssymbol{I-f} --- that may, directly of after reacting, volatilise to the gas phase? + + \section{Reduction of Iodate} + + \Citet{saunders_insights_2012} have shown that \gls{IO3-f} may be reduced when solutions of \gls{IO3-f} and \gls{HAa} are irradiated with \gls{UV-Aa} and \gls{VISa} light between $\gls{LAMBDAs}\geq\qty{310}{\nano\meter}$ and $\gls{LAMBDAs}\approx\qty{780}{\nano\meter}$. The light source was filtered to exclude \gls{IRa} light and lamp output below $\gls{LAMBDAs}=\qty{310}{\nano\meter}$ to simulate the \gls{UV-Aa}-\gls{VISa} solar spectrum in the lower troposphere. They found that the major product of this photochemically induced process was \gls{SOIa} and that the proportion of \gls{I-f} in the reactant solution remained constant at approximately \qty{20}{\percent}. Since \gls{HAa} is a \gls{CHROMOPHOREg}, the suggested mechanism involves photogeneration of solvated electrons \ce{e-(aq)} that, in dependence of \gls{pHs}, yield \gls{HOIf}: \ce{\glssymbol{IO3-f}(aq) + 4e-(aq) + 5\glssymbol{H+f}(aq) ->\glssymbol{HOIf}(aq) + 2\glssymbol{H2Of}(aq)}. From there, \gls{SOIa} may be created through the nucleophilic attack of \gls{HOIf} on diphenolic functional groups \citep{saunders_insights_2012}. Alternatively, \gls{I2f} may be produced through reaction \ref{reac: intro: HOI to I2}, as described by \citet{pillar-little_conversion_2013}: + + \begin{reaction} + \glssymbol{HOIf}(aq) + \glssymbol{I-f} + \glssymbol{H+f}(aq) -> \glssymbol{I2f}(aq) + \glssymbol{H2Of}(l) \label{reac: intro: HOI to I2} + \end{reaction} + Since \gls{I2f} is insoluble \citep{saiz-lopez_atmospheric_2012}, there will be volatilisation of \gls{I2f} to the gas phase. Overall, the mechanism suggested by \citet{saunders_insights_2012} produces primarily \gls{HOIf} \gls{I2f} --- the production pathway of \gls{I-f} has not been elucidated. The presence of \gls{I-f}, however, appears necessary for the production of \ce{\glssymbol{I2f}(g)}. It is hypothetised that \gls{I-f} may be regenerated from \gls{SOIa} \citep{saunders_insights_2012, baker_marine_2005}. Finally, \citet{saunders_insights_2012} have reported oscillations in the release of \ce{\glssymbol{I2f}(g)}. This is likely associated with formation of \gls{H2O2f} as a byproduct of \gls{HAa} photolysis \citep{saunders_insights_2012}. Indeed, \citet{cooper_photochemical_1988} have shown that \gls{H2O2f} is a common product when irradiating aqueous solutions of \glspl{CHROMOPHOREg}. Given \gls{H2O2f}, oscillations in \ce{\glssymbol{I2f}}-\ce{\glssymbol{IO3-f}} are known as the \gls{BRAY-LIEBHAFSKY-MECHANISMa}, first described by \citet{bray_periodic_1921, bray_reactions_1931}: \gls{H2O2f} interacts with \gls{I2f} and \gls{IO3-f} via + + \begin{reactions} + &2\glssymbol{IO3-f}(aq) + 2\glssymbol{H+f}(aq) + 5\glssymbol{H2O2f}(aq) <=> \glssymbol{I2f}(aq) + 5\glssymbol{O2f}(g) + 6\glssymbol{H2Of}(l) \label{reac: oxidation of iodine through hydrogen peroxide}\\ + &\glssymbol{I2f}(aq) + 5\glssymbol{H2O2f}(aq) <=> 2\glssymbol{IO3-f}(aq) + 2\glssymbol{H+f}(aq) + 4\glssymbol{H2Of}(l) \label{reac: reduction of iodate through hydrogen peroxide} + \end{reactions} + to yield a net catalytic decomposition of \gls{H2O2f} via + + \begin{reaction} + 2\glssymbol{H2O2f}(aq) -> 2\glssymbol{H2Of}(l) + \glssymbol{O2f}(g) \label{reac: net catalytic destruction of hydrogen peroxide through iodine-iodate system} + \end{reaction} + The oscillation reaction has a \emph{stable} regime --- here, all species reach steady state except \glssymbol{H2O2f}: likely, \glssymbol{O2f}\ce{(g)} volatilises and \gls{LE-CHATELIER-PRINCIPLEa} dictates that \gls{H2O2f} consequently depletes. The \emph{unstable} regime where either reaction \ref{reac: oxidation of iodine through hydrogen peroxide} or \ref{reac: reduction of iodate through hydrogen peroxide} occur preferrentially, leads to oscillations in \gls{I2f} and \gls{IO3-f}. These oscillations are modulated by initial \gls{pHs} \citep{bray_periodic_1921} and temperature. Including an organic reducing agent and a metal-ion catalyst results in the \gls{BRIGGS-RAUSCHER-MECHANISMa} after \citet{briggs_oscillating_1973}, elucidated by \citet{schmitz_kinetics_2012}: Briefly, in addition to reaction \ref{reac: reduction of iodate through hydrogen peroxide}, the presence of some organic species \ce{R-H2} will induce the following reactions: + + \begin{reactions} + \glssymbol{H+f}(aq) + \glssymbol{IO3-f}(aq) + 2\glssymbol{I2f}(aq) + 5 R-H2(aq) &-> 5 R-HI + 3\glssymbol{H2Of}\\ + \glssymbol{H+f}(aq) + \glssymbol{IO3-f}(aq) + 2\glssymbol{I2f}(aq) + 5 R-HI(aq) &-> 5 R-I2 + 3\glssymbol{H2Of}\\ + R-I2 + R-H2 &<=> 2 R-HI + \end{reactions} + The backward reaction likely proceeds via the metal ion catalyst, although \citet{schmitz_kinetics_2012} reported the possibility of non-catalysed pathways. + + A lot has been learned so far: organic substances may lead to the reduction of \gls{IO3-f}, via \gls{CHROMOPHOREg} activity. Furthermore, observed oscillations in gas phase \ce{\glssymbol{I2f}} may be explained through \gls{BRAY-LIEBHAFSKY-MECHANISMa}-\gls{BRIGGS-RAUSCHER-MECHANISMa} mechanisms. However, the suitability of \glspl{HAa} to represent organic aerosol has been questioned: \citet{graber_atmospheric_2006} suggested that humic-like substances found in aerosol particles may differ substantially from humic substances found in soil. More specifically, \citet{graber_atmospheric_2006} argue that terrestrial sources --- from which the \gls{HAa} used by \citet{saunders_insights_2012} likely originate --- may not be the origin of the majority of humic-like substances in aerosol. Differences may be found in terms of molecular weight, aromatic moiety content, surface properties and other properties \citep{graber_atmospheric_2006}. Although \glspl{HAa} as organics have profen useful to elucidate the mechanisms of \glssymbol{I2f} recycling, quantitatively constraining this recycling better requires more realistic organics. Another important question to answer, therefore, is: are there proxies that represent organics in aerosol more accurately, and to which the same \gls{CHROMOPHOREg}-dependent pathway of iodine recycling applies? + + \section{Reduction of Iodate: Proxies for Secondary Organic Aerosol} + + \Citet{guenther_global_1995} modelled global natural \gls{VOCa} emissions in 1990. They found a total flux of $\qty{1150}{\tera\gramCarbon\per\year}$, of which \qty{44}{\percent} (\qty{503}{\tera\gramCarbon\per\year}) was \gls{ISOPRENEf} and \qty{11}{\percent} (\qty{127}{\tera\gramCarbon\per\year}) were monoterpenes such as \gls{A-PINENEf}. Thereof, approximately \qty{75}{\percent} orginated from forests. In 2006, The annual atmospheric \gls{VOCa} injection was further specified in 2012 when \citet{guenther_model_2012} reported the following emissions of \glspl{VOCa} for the year 2000: total emissions were \qty{1089}{\tera\gramCarbon\per\year}, of which \gls{ISOPRENEf} emissions were \qty{49.1}{\percent} (\qty{535}{\tera\gramCarbon\per\year}) and the monoterpenes \gls{A-PINENEf}, \gls{B-PINENEf} and \gls{LIMONENEf} contributed \qty{6.7}{\percent} (\qty{66.1}{\tera\gramCarbon\per\year}), \qty{1.7}{\percent} (\qty{18.9}{\tera\gramCarbon\per\year}) and \qty{1.0}{\percent} (\qty{11.4}{\tera\gramCarbon\per\year}), respectively. \gls{ISOPRENEf} and monoterpene emissions are biogenic and mostly linked to vegetation --- overall they contributed approximately \qty{65}{\percent} to global \gls{VOCa} emissions in 2000 \citep{guenther_model_2012}, rendering them a major source of atmospheric \glspl{VOCa}. + + Organic matter in aerosol is present either as \gls{POAa} or \gls{SOAa}. \gls{POAa} and \gls{SOAa} comprise the largest share of \emph{fine} particles with diameters $d\leq\qty{2.5}{\micro\meter}$. On the other hand, large particles with diameters $d>\qty{2.5}{\micro\meter}$ are mostly comprised of particles formed mechanically, including soil and mineral dust, sea salt particles and plant particles \citep{jziemann_kinetics_2012}. \gls{POAa} requires no chemical reactions to condense to the aerosol phase. Conversely, \gls{SOAa} is created when volatile precursor species are chemically altered to lower volatilities, and consequently condense to the aerosol phase. Likely, \gls{SOAa} constitues a large fraction of organic aerosol \cite{bianchi_highly_2019, hallquist_formation_2009}. As a general rule of thumb, higher oxygen content of a molecule indicates \emph{lower} volatility. Therefore, oxidation reactions are highly important in \gls{SOAa} formation because oxidation effectively \emph{decreases} volatility. Recent work summarised by \citet{bianchi_highly_2019} suggests that there exists class of of low-volatile species referred to as \glspl{HOMa} with low volatility. Such \glspl{HOMa} are formed through \emph{autooxidation} reactions involving peroxy radicals: this process is detailed by \citet{bianchi_highly_2019}, and the subtle but important difference between \glspl{HOMa} and molecules with high oxygen content is laid out. Briefly, \glspl{HOMa} are species of very low vapour pressure so that condensation onto existing particles is very probable and almost irreversible \citep{bianchi_highly_2019}. High yields of \glspl{HOMa} have been observed for \gls{ISOPRENEf} and the monoterpenes \gls{A-PINENEf} and especially \gls{LIMONENEf} \citep{bianchi_highly_2019}, with total yields of \qty{4}{\percent} (\gls{ISOPRENEf}), \qtyrange{7.0\pm3.5}{3.4\pm1.0}{\percent} (\gls{A-PINENEf}) and \qty{17.0\pm8.5}{\percent} (\gls{LIMONENEf}), respectively \citep{bianchi_highly_2019, jokinen_production_2015, ng_secondary_2008, ehn_large_2014, kirkby_ion-induced_2016}. It may therefore be assumed that derivatives --- or more precisely oxidation products --- of monoterpenes or \gls{ISOPRENEf} are common in \gls{SOAa}. Building on the work of \citet{saunders_insights_2012}, chosing an oxidation product of \gls{ISOPRENEf} or monoterpenes as the investigated organics may constitute a more realistc proxy for aerosol organics. + + Recently, \citet{reza_iodine_2024} have performed similar experiments as \citet{saunders_insights_2012}, but using organic species better representing \gls{VOCa} oxidation. Recent observations have shown elevated concentrations of \ce{\glssymbol{IO.f}(g)} in dust layers above the Atacama and Sechura deserts: \citet{koenig_ozone_2021} measured a ten-fold enhancement of \gls{IO.f} concentrations compared to the regional background signal of \qtyrange{0.10}{0.25}{\pptv}. Because iron is hypothetised to catalyse photochemistry in dust particles, and since it is the most abundant transition metal in dust minerals \citep{aal-abadleh_perspective_2023}, iron may serve as a proxy for dust when investigating the reduction of \gls{IO3-f}. In a series of \gls{CWFTRa} experiments, \citet{reza_iodine_2024} used a \gls{CE-DOASa} to detect \glssymbol{I2f}\ce{(g)} and a \gls{ToF I-CIMSa} to detect \glspl{OVOCa} associated with \gls{IO3-f} reduction in thin aqueous films. The films were inserted into the \gls{CWFTRa} and consisted of an organic or inorganic matrix and \gls{IO3-f}. + The organic matrices included \gls{IRON-3-CITRATEa}, \gls{CAa} and \gls{BTCAa}. \gls{CAa} was found in aerosol \citep{lienhard_measurements_2012} and is a proxy for oxygenated organic species. \gls{IRON-3-CITRATEa}, as a known photoactive compound, is considered a suitable proxy for \ce{Fe}(\toRoman{3}) carboxylate complexes found in the atmosphere \citep{reza_iodine_2024}. Importantly, \gls{CAa} has well-characterised hygroscopic properties \citep{reza_iodine_2024} so that this matrix can be used to control against \glspl{MATRIX-EFFECT-(CHEM)g} of organics that are due to iron when using \gls{IRON-3-CITRATEa}. These matrices were mixed with a solution of \gls{NaIO3f} to introduce \gls{IO3-f} at a concentration of $\approx\qty{30}{\milli\Molar}$. The results show that irradiation with \gls{VISa} for films containing \gls{IRON-3-CITRATEa} led to the reduction of $\approx\qty{40}{\percent}$ of the initially present \gls{IO3-f}. Likely, \gls{IRON-3-CITRATEa} undergoes a \gls{LMCTa} induced through irradiance with a photon at $\lambda<\qty{500}{\nano\meter}$ to yield \gls{CITRATEa} radicals and solvated electrons \ce{e-(aq)}, as described by \citet{saunders_insights_2012}. Likely, reduction of \gls{IO3-f} is driven through these solvated electrons. Furthermore, \citet{reza_iodine_2024} report that the speciation of the \glspl{CHROMOPHOREg} may include iodine-containing compounds. + +\end{document} \ No newline at end of file diff --git a/chapters/methods.ist b/chapters/methods.ist new file mode 100644 index 0000000..aacc978 --- /dev/null +++ b/chapters/methods.ist @@ -0,0 +1,29 @@ +% makeindex style file created by the glossaries package +% for document 'methods' on 2026-8-11 +actual '?' +encap '|' +level '!' +quote '"' +keyword "\\glossaryentry" +preamble "\\glossarysection[\\glossarytoctitle]{\\glossarytitle}\\glossarypreamble\n\\begin{theglossary}\\glossaryheader\n" +postamble "\%\n\\end{theglossary}\\glossarypostamble\n" +group_skip "\\glsgroupskip\n" +item_0 "\%\n" +item_1 "\%\n" +item_2 "\%\n" +item_01 "\%\n" +item_x1 "\\relax \\glsresetentrylist\n" +item_12 "\%\n" +item_x2 "\\relax \\glsresetentrylist\n" +delim_0 "\{\\glossaryentrynumbers\{\\relax " +delim_1 "\{\\glossaryentrynumbers\{\\relax " +delim_2 "\{\\glossaryentrynumbers\{\\relax " +delim_t "\}\}" +delim_n "\\delimN " +delim_r "\\delimR " +headings_flag 1 +heading_prefix "\\glsgroupheading\{" +heading_suffix "\}\\relax \\glsresetentrylist " +symhead_positive "glssymbols" +numhead_positive "glsnumbers" +page_compositor "." diff --git a/chapters/methods.pdf b/chapters/methods.pdf new file mode 100644 index 0000000..a8b6a18 Binary files /dev/null and b/chapters/methods.pdf differ diff --git a/chapters/methods.tex b/chapters/methods.tex new file mode 100644 index 0000000..d95bbe2 --- /dev/null +++ b/chapters/methods.tex @@ -0,0 +1,53 @@ +% !TeX program = lualatex + +%% ------------------------------------------------------------------% +%% SUBFILE MODE +\documentclass[../main/main.tex]{subfiles} +\graphicspath{{../graphics/}} + + +%% ------------------------------------------------------------------% +%% DOCUMENT + + +\begin{document} + + \pagestyle{mainbody} + + \chapter{Methods} + \thispagestyle{mainbody} + + We use a sequential workflow outlined in figure \ref{methods: fig: overview over workflow}. + + \begin{figure}[h] + \centering + \includegraphics{flowcharts/method_overview.pdf} + \caption[Overview over Workflow]{\textbf{Overview over Workflow}. The initial step consists of producing a filter containing \gls{VOCa} in the \gls{OFRa}, which is subsequently extracted to produce a solution. } + \label{methods: fig: overview over workflow} + \end{figure} + + \section{Oxidation Flow Reactor} + + \begin{figure}[h] + \centering + \includegraphics{flowcharts/OFR_Flowchart.pdf} + \caption[Overview over OFR Flowchart]{\textbf{Overview over OFR Flowchart}. Flow Chart displaying the functionality of the OFR Setup, including various flows, instruments, diverse valves and other things.} + \end{figure} + + \section{Filter TOC Measurement} + + \begin{figure} + \centering + \includegraphics{processes/solution_creation.pdf} + \caption[Procedure to create solutions]{Procedure to create solutions. Beaker apapted from: Diogo Losch De Oliveira (2026). Beakers [Illustration]. CC-BY 4.0. SciDraw.io. https://scidraw.io/drawing/beakers-ba8583ed, accessed 10. August 16:16} + \label{methods: fig: solution preparation} + \end{figure} + + \section{Preparation of coating solution} + + + \section{Coated Wall Flow Tube experiment} + + \section{Data Analysis} + +\end{document} \ No newline at end of file diff --git a/chapters/results.tex b/chapters/results.tex new file mode 100644 index 0000000..ed2c5c2 --- /dev/null +++ b/chapters/results.tex @@ -0,0 +1,85 @@ +% !TeX program = lualatex + +%% ------------------------------------------------------------------% +%% SUBFILE MODE +\documentclass[../main/main.tex]{subfiles} +\graphicspath{{../graphics/}} + + +%% ------------------------------------------------------------------% +%% DOCUMENT + + +\begin{document} + + \pagestyle{mainbody} + + \chapter{Introduction} + \thispagestyle{mainbody} + + + Iodine is the heaviest stable halogen element with atomic number \qty{53}{}. It has an average atomic weight of \qty{126.904}{\amu} and forms a semi-lustrous solid under standard conditions (here \qty{273.15}{\kelvin} and \qty{1}{\bar}, see \citet{calvert_glossary_1990}) \citep{kaiho_physical_2015}. Its melting and boiling points are \qty{114}{\degreeCelsius} and \qty{184}{\degreeCelsius}, respectively, and its vapour pressure is \qty{0.031}{\kilo\pascal} and \qty{9.17}{\kilo\pascal} at \qty{25}{\degreeCelsius} and \qty{113.6}{\degreeCelsius}, respectively \citep{kaiho_physical_2015}. The atomic radius of iodine is \qty{140}{\pico\meter} and its first ionisation energy is \qty{1015}{\kilo\joule\per\mol} \citep{kaiho_physical_2015}. Iodine is important in the enviornment: in the atmosphere, it influences the chemistry of ozone and important radical species, and it may be cause the formation of particles that may act as nuclei for aerosol or clouds \citep{saiz-lopez_atmospheric_2012}. The former is important for the capability of the atmophere to oxidise and remove species emitted to it, while the latter is important because of its effect on radiative equilibrium of Earth. + + \section{Iodine in the environment} + + Iodine is litophilic and incompatible in Earth's astenosphere, and therefore concentrated in oceans and surface sediments \citep{kendrick_halogen_2024}. Marine sediments constitute the largest iodine reservoir \citep{kendrick_halogen_2024} with much higher concentrations of \qtyrange{20}{600}{\milli\gram\per\kilogram} compared to soil- (\qtyrange{0.5}{20}{\milli\gram\per\kilogram}) or rock (\qtyrange{0.08}{0.5}{\milli\gram\per\kilogram}) concentrations \citep{whitehead_distribution_1984}. Sedimented iodine may be recycled into the oceans through sedimentary brines \citep{muramatsu_recycling_2001, muramatsu_studies_2004} around techtonically active subduction zones \citep{carrano_influence_2020} through diagenesis processes involving thermal decompostion or microbiological reduction of buried organic matter \citep{kendrick_halogen_2024, muramatsu_recycling_2001}. Consequently, iodine concentrations in the oceans are approximately \qtyrange{45}{60}{\micro\gram\per\liter} \citep{whitehead_distribution_1984}, mostly in the form of \gls{IO3-f}, the thermodynamically most stable state of iodine in aqueous solution \citep{fuge_iodine_2015}. However, \gls{IO3-f} exhibits a nutrient-like profile \citep{carrano_influence_2020} being depleted at the surface, whereas \gls{I-f} is enriched in the surface \citep{elderfield_biophilic_1980}. Similarly, organic matter is enriched in the surface, so that the existence of some iodinated organics may be presumed \citep{saiz-lopez_atmospheric_2012}. Within the oceans, iodine is incorporated preferrentially in organic matter \citep{kendrick_halogen_2024} by micro- and macroalgae, and aerobic bacteria \citep{carpenter_biogeochemical_2015}: through faciliated diffusion (see detailed descriptions in \citet{kupper_iodide_2008, winter_exploring_2009, amachi_microbial_2008}), cells store iodine as \ce{\glssymbol{I-f}(aq)} or associated to organic molecules \citep{kupper_iodide_2008, amachi_microbial_2008}. + \Gls{I-f} within the cell interior may act as an antioxidant \citep{kupper_iodide_2008}: upon oxidative stress, the \gls{I-f} reservoir is mobilised and cells emit \ce{\glssymbol{I-f}(aq)} and a range of \glspl{VOICa} \citep{kupper_iodide_2008, carpenter_biogeochemical_2015} that may volatilise to the atmosphere. Analogously, when oxidative stress occurs during air exposure at low tide, the hetergeneous surface reaction of \gls{I-f} and \gls{O3f} at the sea-water interface produces \gls{HOIf}, \gls{I2f} and \glspl{IO.f} directly emitted to the atmosphere \citep{carpenter_biogeochemical_2015, palmer_iodine_2005, liu_kinetics_2001, sakamoto_direct_2009, hayase_heterogeneous_2010, he_role_2021}. It is currently thought that the biggest source of inorganic iodine to the atmosphere is \gls{HOIf} produced via the same pathway, exceeding the emissions of \gls{I2f} by one order of magnitude \citep{carpenter_atmospheric_2013}. + Nevertheless, the atmospheric iodine budget is currently not well-constrained \citep{saiz-lopez_atmospheric_2012}. \glspl{VOICa} (notably \ce{\glssymbol{CH3If}}) and inorganic iodine species (\ce{\glssymbol{HOIf}}, \ce{\glssymbol{I2f}}, \ce{\glssymbol{IO.f}}) emitted from the oceans constitute the biggest source of iodine to the atmosphere \citep{carpenter_biogeochemical_2015, carpenter_atmospheric_2013}, with estimated input $\approx\qty{550}{\giga\gram\per\year}$ \citep{saiz-lopez_atmospheric_2012}. Most \glspl{VOICa} are photolabile with lifetimes on the order of minutes to days \citep{bloss_kinetics_2001}. Other natural sources of iodine to the amtosphere include soils and plants \citep{whitehead_distribution_1984, carpenter_biogeochemical_2015, fuge_iodine_2015}, terrestrial water systems \citep{whitehead_distribution_1984}, and volcanoes or salt lakes \citep{carpenter_biogeochemical_2015}. The additional input from terrestrial sources into the atmosphere is $\approx\qtyrange{80}{110}{\giga\gram\per\year}$ \citep{saiz-lopez_atmospheric_2012}. Anthropogenic sources include direct emissions from fossil fuel burning \citep{fuge_iodine_2015} and pesticide use \citep{zheng_accelerated_2003, whitehead_distribution_1984}. There are indirect anthropogenic effects as well: ice core data indicates that the sea-air flux of iodine has tripled between 1950 and 2010 as a consequence of increased anthropogenic ozone pollution of the troposphere \citep{cuevas_rapid_2018}. Sinks of atmospheric iodine include wet- and dry deposition \citep{fuge_iodine_2015}, and direct uptake through plants \citep{fuge_iodine_2015}. Overall, this leads to boundary layer mixing ratios of $\chi_{\ce{\glssymbol{I2f}(g)}}\leq\qty{93}{\pptv}$ \citep{carpenter_biogeochemical_2015}, $\chi_{\ce{\glssymbol{IO.f}(g)}}\leq\qtyrange{3}{20}{\pptv}$ \citep{carpenter_biogeochemical_2015}, $\chi_{\ce{\glssymbol{HOIf}(g)}}\leq\qty{1}{\pptv}$ \citep{he_role_2021} and $\chi_{\ce{\glssymbol{I.f}(g)}}\leq\qtyrange{0.1}{22}{\pptv}$ \citep{carpenter_biogeochemical_2015, he_role_2021}. + + \section{Iodine Chemistry in the Atmosphere} + + The importance of the marine iodine source is likely also reflected in aerosol composition: above marine areas, aerosol is enriched in iodine relative to seawater content by a factor of \qtyrange{100}{1000}{} \citep{carpenter_biogeochemical_2015}. Iodine may be transported into the aerosol phase through bubble-bursting of iodine-rich surface ocean waters \citep{saiz-lopez_atmospheric_2012}, or through the formation of aerosol via \glspl{IOPa} \citep{odowd_marine_2002}. Likely, low-volatility iodinated organics may also condense into the aerosol phase. Overall, various iodinated species may be present in aerosol including \gls{I-f}, \gls{IO3-f}, \gls{HOIf} and \gls{SOIa} \citep{saiz-lopez_atmospheric_2012}. \Citet{saiz-lopez_atmospheric_2012, gilfedder_iodine_2008} report that \gls{SOIa} is very frequent in aerosol and may constitute the largest reservoir of iodine in aerosol. There appear to be two principal pathways of \gls{SOIa} accomodation: direct accumulation from sea spray enriched in iodinated organics, and the reaction of \gls{HOIf} with aerosol organics. \Gls{HOIf} may also be highly reactive towards other species, likely due to its affinity for nucelophilic attacks on susceptible species. In general however, \gls{HOIf} or other likewise reduced iodine species such as \gls{I-f} should be oxidised to \gls{IO3-f} \citep{gilfedder_iodine_2008}, the thermodynamically most stable form of iodine in aqueous solution. Consequently, the accumulated form of iodine in condensed aerosol phases is often thought to be \gls{IO3-f} \citep{gilfedder_iodine_2008, saiz-lopez_atmospheric_2012}. However, observations in the troposphere indicate higher aerosol contents of \gls{I-f} than \gls{IO3-f} \citep{gilfedder_iodine_2008}, or high variability in the \gls{I-f}/\gls{IO3-f} ratio \citep{saiz-lopez_atmospheric_2012}. This indicates the presence of a mechanism reducing \gls{IO3-f} in the troposphere. + + Hetergeneous aerosol chemistry of iodine is closely linked to homogeneous chemistry of iodine through many iodine species. Generally, atmospheric iodine chemistry is initiated mostly through \gls{RISa} such as \glspl{I.f} or \glspl{IO.f}. Briefly, homogeneous iodine chemistry involves catalytic destruction of troposheric ozone via various pathways involving \glspl{HOxf} and \glspl{NOxf} as well as other halogen atoms in the atmosphere \citep{saiz-lopez_reactive_2012}. This process is photochemically driven and initiated with \glssymbol{IO.f} and \glssymbol{I.f}. \citet{saiz-lopez_reactive_2012} have outlined the mechanism: the intial step is the production of \glspl{I.f} from \glspl{RInf} or \gls{I2f}. The \glspl{I.f} react with \gls{O3f} to produce \glspl{IO.f} that in turn recombine to again produce \glspl{I.f}: + + \begin{reactions} + \RI{}(g) + ${h\nu}$ &-> R^{\bullet}(g) + \glssymbol{I.f}(g)\\ + \glssymbol{I2f}(g) + ${h\nu}$ &-> 2 \glssymbol{I.f}(g)\\ + \glssymbol{I.f}(g) + \glssymbol{O3f}(g) &-> \glssymbol{IO.f}(g) + \glssymbol{O2f}(g) \label{reac: intro: iodine radical ozone loss}\\ + 2\glssymbol{IO.f} &-> 2\glssymbol{I.f}(g) + \glssymbol{O2f}(g)\label{reac: intro: 2IO to 2I and O2} + \end{reactions} + The net outcome is ozone destruction with \ce{2\glssymbol{O3f}(g) -> 3\glssymbol{O2f}(g)}, although reaction \ref{reac: intro: 2IO to 2I and O2} has other channels that may involve \glssymbol{HOxf} and \glssymbol{NOxf} cycles. Importantly, the \gls{IO.f} has a lifetime against photolysis in the boundary layer on the order of seconds \citep{bloss_kinetics_2001}. Likewise, the effective lifetime of \gls{Ix.f} against uptake in aerosol is on the order of hours \citep{dix_detection_2013}: sustained presence of \glspl{IO.f} in the atmosphere therefore requires an effective recycling mechanism for \ce{\glssymbol{IO.f}}. + + Additionally, iodine may be involved in the oxidation of atmospheric organic molecules or mercury, allowing the latter to enter the food chain as highly poisonous methylmercury \citep{steffen_synthesis_2008, saiz-lopez_reactive_2012, saiz-lopez_atmospheric_2012}, and likely leading to enhanced condensation of organics into the aerosol phase through the former. Further, through formation of \glspl{IOPa}, iodine oxides may lead to the production of \glspl{UFAPa} \citep{carpenter_biogeochemical_2015}. Volatile species may condense on \glspl{UFAPa} that can grow up to the point of becoming \glspl{CCNa} \citep{saiz-lopez_atmospheric_2012}. Recent evidence shows that nucleation via iodine oxoacids to produce \glspl{IOPa} is highly efficient and sometimes competitive with sulfuric acid-ammonium driven nucleation \citep{he_role_2021}. Moreover, heterogeneous iodine chemistry on pre-existing frozen or liquid salt particles may lead to sudden increases in gas phase iodine species \citep{saiz-lopez_reactive_2012}. Importantly, the reaction of \gls{Br-f} with \gls{O3f} on frozen salt solutions occurs in the brine pertaining to the bulk ice phase, rather than \emph{within} the bulk ice phase \citep{oldridge_formation_2011}: such brines are formed when freezing solutions exclude solutes --- the heterogeneous reaction of \gls{O3f} with \gls{I-f} on frozen aerosol is here assumed to behave similarly. In other words, the heterogeneous reaction of \gls{O3f} with aerosol surfaces is assumed to be similar for frozen and liquid aerosol particles. + + Other heterogeneous effects may lead to substantial iodine emissions through the reaction of ozone with dissolved \gls{I-f} in ocean and aerosols \citep{palmer_iodine_2005, liu_kinetics_2001, sakamoto_direct_2009, hayase_heterogeneous_2010}. In the upper troposphere and lower stratosphere, heterogeneous recycling of iodine species is highly important: Model calculations by \citet{saiz-lopez_injection_2015} show that from the lower troposphere, convection may transport inorganic- and organic iodine species to the lower stratosphere, causing a \gls{Iyf} injection of \qtyrange{0.25}{0.7}{\pptv} \citep{saiz-lopez_injection_2015}. Measurements by \citet{koenig_quantitative_2020} are in agreement with this, indicating an injection of \qty{0.77\pm0.10}{\pptv} of \glssymbol{Iyf} into the lower stratosphere. Associated therewith is a mixing ratio of $\chi_{\ce{\glssymbol{IO.f}(g)}}=\qty{0.06\pm0.03}{\pptv}$ even for aged stratospheric air. \Citet{koenig_quantitative_2020} also observed that increases in altitude across the troposphere are associated with (1) an increase in particulate iodine and a decrease in gas phase iodine; and (2) a shift of \gls{I-f}-\gls{IO3-f} speciation in the condensed phase towards \gls{IO3-f}. Simulations could reproduce observed $\chi_{\ce{\glssymbol{IO.f}(g)}}$ only when a recycling scheme for iodine on ice particles was applied, and when the proper partioning between condensed- and gas phase was applied. This indicates that, as for the troposphere, a recycling mechanism producing gas phase \glspl{IO.f} must exist. There is also evidence that \gls{IO3-f} should be reduced to \gls{I-f}: \citet{pillar-little_conversion_2013} have established a pathway through which \gls{I-f} and \gls{O3f} cause volatilization of \ce{\glssymbol{I2f}(g)} and \ce{\glssymbol{HOIf}(g)} from watery microdroplets. However, it is still unclear \emph{how} the necessary \gls{I-f} is formed, given that most iodine should be present as \gls{IO3-f}. Consequently, an important question to answer is: how is \glssymbol{IO3-f} reduced to species --- most likely \glssymbol{I-f} --- that may, directly of after reacting, volatilise to the gas phase? + + \section{Reduction of Iodate} + + \Citet{saunders_insights_2012} have shown that \gls{IO3-f} may be reduced when solutions of \gls{IO3-f} and \gls{HAa} are irradiated with \gls{UV-Aa} and \gls{VISa} light between $\gls{LAMBDAs}\geq\qty{310}{\nano\meter}$ and $\gls{LAMBDAs}\approx\qty{780}{\nano\meter}$. The light source was filtered to exclude \gls{IRa} light and lamp output below $\gls{LAMBDAs}=\qty{310}{\nano\meter}$ to simulate the \gls{UV-Aa}-\gls{VISa} solar spectrum in the lower troposphere. They found that the major product of this photochemically induced process was \gls{SOIa} and that the proportion of \gls{I-f} in the reactant solution remained constant at approximately \qty{20}{\percent}. Since \gls{HAa} is a \gls{CHROMOPHOREg}, the suggested mechanism involves photogeneration of solvated electrons \ce{e-(aq)} that, in dependence of \gls{pHs}, yield \gls{HOIf}: \ce{\glssymbol{IO3-f}(aq) + 4e-(aq) + 5\glssymbol{H+f}(aq) ->\glssymbol{HOIf}(aq) + 2\glssymbol{H2Of}(aq)}. From there, \gls{SOIa} may be created through the nucleophilic attack of \gls{HOIf} on diphenolic functional groups \citep{saunders_insights_2012}. Alternatively, \gls{I2f} may be produced through reaction \ref{reac: intro: HOI to I2}, as described by \citet{pillar-little_conversion_2013}: + + \begin{reaction} + \glssymbol{HOIf}(aq) + \glssymbol{I-f} + \glssymbol{H+f}(aq) -> \glssymbol{I2f}(aq) + \glssymbol{H2Of}(l) \label{reac: intro: HOI to I2} + \end{reaction} + Since \gls{I2f} is insoluble \citep{saiz-lopez_atmospheric_2012}, there will be volatilisation of \gls{I2f} to the gas phase. Overall, the mechanism suggested by \citet{saunders_insights_2012} produces primarily \gls{HOIf} \gls{I2f} --- the production pathway of \gls{I-f} has not been elucidated. The presence of \gls{I-f}, however, appears necessary for the production of \ce{\glssymbol{I2f}(g)}. It is hypothetised that \gls{I-f} may be regenerated from \gls{SOIa} \citep{saunders_insights_2012, baker_marine_2005}. Finally, \citet{saunders_insights_2012} have reported oscillations in the release of \ce{\glssymbol{I2f}(g)}. This is likely associated with formation of \gls{H2O2f} as a byproduct of \gls{HAa} photolysis \citep{saunders_insights_2012}. Indeed, \citet{cooper_photochemical_1988} have shown that \gls{H2O2f} is a common product when irradiating aqueous solutions of \glspl{CHROMOPHOREg}. Given \gls{H2O2f}, oscillations in \ce{\glssymbol{I2f}}-\ce{\glssymbol{IO3-f}} are known as the \gls{BRAY-LIEBHAFSKY-MECHANISMa}, first described by \citet{bray_periodic_1921, bray_reactions_1931}: \gls{H2O2f} interacts with \gls{I2f} and \gls{IO3-f} via + + \begin{reactions} + &2\glssymbol{IO3-f}(aq) + 2\glssymbol{H+f}(aq) + 5\glssymbol{H2O2f}(aq) <=> \glssymbol{I2f}(aq) + 5\glssymbol{O2f}(g) + 6\glssymbol{H2Of}(l) \label{reac: oxidation of iodine through hydrogen peroxide}\\ + &\glssymbol{I2f}(aq) + 5\glssymbol{H2O2f}(aq) <=> 2\glssymbol{IO3-f}(aq) + 2\glssymbol{H+f}(aq) + 4\glssymbol{H2Of}(l) \label{reac: reduction of iodate through hydrogen peroxide} + \end{reactions} + to yield a net catalytic decomposition of \gls{H2O2f} via + + \begin{reaction} + 2\glssymbol{H2O2f}(aq) -> 2\glssymbol{H2Of}(l) + \glssymbol{O2f}(g) \label{reac: net catalytic destruction of hydrogen peroxide through iodine-iodate system} + \end{reaction} + The oscillation reaction has a \emph{stable} regime --- here, all species reach steady state except \glssymbol{H2O2f}: likely, \glssymbol{O2f}\ce{(g)} volatilises and \gls{LE-CHATELIER-PRINCIPLEa} dictates that \gls{H2O2f} consequently depletes. The \emph{unstable} regime where either reaction \ref{reac: oxidation of iodine through hydrogen peroxide} or \ref{reac: reduction of iodate through hydrogen peroxide} occur preferrentially, leads to oscillations in \gls{I2f} and \gls{IO3-f}. These oscillations are modulated by initial \gls{pHs} \citep{bray_periodic_1921} and temperature. Including an organic reducing agent and a metal-ion catalyst results in the \gls{BRIGGS-RAUSCHER-MECHANISMa} after \citet{briggs_oscillating_1973}, elucidated by \citet{schmitz_kinetics_2012}: Briefly, in addition to reaction \ref{reac: reduction of iodate through hydrogen peroxide}, the presence of some organic species \ce{R-H2} will induce the following reactions: + + \begin{reactions} + \glssymbol{H+f}(aq) + \glssymbol{IO3-f}(aq) + 2\glssymbol{I2f}(aq) + 5 R-H2(aq) &-> 5 R-HI + 3\glssymbol{H2Of}\\ + \glssymbol{H+f}(aq) + \glssymbol{IO3-f}(aq) + 2\glssymbol{I2f}(aq) + 5 R-HI(aq) &-> 5 R-I2 + 3\glssymbol{H2Of}\\ + R-I2 + R-H2 &<=> 2 R-HI + \end{reactions} + The backward reaction likely proceeds via the metal ion catalyst, although \citet{schmitz_kinetics_2012} reported the possibility of non-catalysed pathways. + + A lot has been learned so far: organic substances may lead to the reduction of \gls{IO3-f}, via \gls{CHROMOPHOREg} activity. Furthermore, observed oscillations in gas phase \ce{\glssymbol{I2f}} may be explained through \gls{BRAY-LIEBHAFSKY-MECHANISMa}-\gls{BRIGGS-RAUSCHER-MECHANISMa} mechanisms. However, the suitability of \glspl{HAa} to represent organic aerosol has been questioned: \citet{graber_atmospheric_2006} suggested that humic-like substances found in aerosol particles may differ substantially from humic substances found in soil. More specifically, \citet{graber_atmospheric_2006} argue that terrestrial sources --- from which the \gls{HAa} used by \citet{saunders_insights_2012} likely originate --- may not be the origin of the majority of humic-like substances in aerosol. Differences may be found in terms of molecular weight, aromatic moiety content, surface properties and other properties \citep{graber_atmospheric_2006}. Although \glspl{HAa} as organics have profen useful to elucidate the mechanisms of \glssymbol{I2f} recycling, quantitatively constraining this recycling better requires more realistic organics. Another important question to answer, therefore, is: are there proxies that represent organics in aerosol more accurately, and to which the same \gls{CHROMOPHOREg}-dependent pathway of iodine recycling applies? + + \section{Reduction of Iodate: Proxies for Secondary Organic Aerosol} + + \Citet{guenther_global_1995} modelled global natural \gls{VOCa} emissions in 1990. They found a total flux of $\qty{1150}{\tera\gramCarbon\per\year}$, of which \qty{44}{\percent} (\qty{503}{\tera\gramCarbon\per\year}) was \gls{ISOPRENEf} and \qty{11}{\percent} (\qty{127}{\tera\gramCarbon\per\year}) were monoterpenes such as \gls{A-PINENEf}. Thereof, approximately \qty{75}{\percent} orginated from forests. In 2006, The annual atmospheric \gls{VOCa} injection was further specified in 2012 when \citet{guenther_model_2012} reported the following emissions of \glspl{VOCa} for the year 2000: total emissions were \qty{1089}{\tera\gramCarbon\per\year}, of which \gls{ISOPRENEf} emissions were \qty{49.1}{\percent} (\qty{535}{\tera\gramCarbon\per\year}) and the monoterpenes \gls{A-PINENEf}, \gls{B-PINENEf} and \gls{LIMONENEf} contributed \qty{6.7}{\percent} (\qty{66.1}{\tera\gramCarbon\per\year}), \qty{1.7}{\percent} (\qty{18.9}{\tera\gramCarbon\per\year}) and \qty{1.0}{\percent} (\qty{11.4}{\tera\gramCarbon\per\year}), respectively. \gls{ISOPRENEf} and monoterpene emissions are biogenic and mostly linked to vegetation --- overall they contributed approximately \qty{65}{\percent} to global \gls{VOCa} emissions in 2000 \citep{guenther_model_2012}, rendering them a major source of atmospheric \glspl{VOCa}. + + Organic matter in aerosol is present either as \gls{POAa} or \gls{SOAa}. \gls{POAa} and \gls{SOAa} comprise the largest share of \emph{fine} particles with diameters $d\leq\qty{2.5}{\micro\meter}$. On the other hand, large particles with diameters $d>\qty{2.5}{\micro\meter}$ are mostly comprised of particles formed mechanically, including soil and mineral dust, sea salt particles and plant particles \citep{jziemann_kinetics_2012}. \gls{POAa} requires no chemical reactions to condense to the aerosol phase. Conversely, \gls{SOAa} is created when volatile precursor species are chemically altered to lower volatilities, and consequently condense to the aerosol phase. Likely, \gls{SOAa} constitues a large fraction of organic aerosol \cite{bianchi_highly_2019, hallquist_formation_2009}. As a general rule of thumb, higher oxygen content of a molecule indicates \emph{lower} volatility. Therefore, oxidation reactions are highly important in \gls{SOAa} formation because oxidation effectively \emph{decreases} volatility. Recent work summarised by \citet{bianchi_highly_2019} suggests that there exists class of of low-volatile species referred to as \glspl{HOMa} with low volatility. Such \glspl{HOMa} are formed through \emph{autooxidation} reactions involving peroxy radicals: this process is detailed by \citet{bianchi_highly_2019}, and the subtle but important difference between \glspl{HOMa} and molecules with high oxygen content is laid out. Briefly, \glspl{HOMa} are species of very low vapour pressure so that condensation onto existing particles is very probable and almost irreversible \citep{bianchi_highly_2019}. High yields of \glspl{HOMa} have been observed for \gls{ISOPRENEf} and the monoterpenes \gls{A-PINENEf} and especially \gls{LIMONENEf} \citep{bianchi_highly_2019}, with total yields of \qty{4}{\percent} (\gls{ISOPRENEf}), \qtyrange{7.0\pm3.5}{3.4\pm1.0}{\percent} (\gls{A-PINENEf}) and \qty{17.0\pm8.5}{\percent} (\gls{LIMONENEf}), respectively \citep{bianchi_highly_2019, jokinen_production_2015, ng_secondary_2008, ehn_large_2014, kirkby_ion-induced_2016}. It may therefore be assumed that derivatives --- or more precisely oxidation products --- of monoterpenes or \gls{ISOPRENEf} are common in \gls{SOAa}. Building on the work of \citet{saunders_insights_2012}, chosing an oxidation product of \gls{ISOPRENEf} or monoterpenes as the investigated organics may constitute a more realistc proxy for aerosol organics. + + Recently, \citet{reza_iodine_2024} have performed similar experiments as \citet{saunders_insights_2012}, but using organic species better representing \gls{VOCa} oxidation. Recent observations have shown elevated concentrations of \ce{\glssymbol{IO.f}(g)} in dust layers above the Atacama and Sechura deserts: \citet{koenig_ozone_2021} measured a ten-fold enhancement of \gls{IO.f} concentrations compared to the regional background signal of \qtyrange{0.10}{0.25}{\pptv}. Because iron is hypothetised to catalyse photochemistry in dust particles, and since it is the most abundant transition metal in dust minerals \citep{aal-abadleh_perspective_2023}, iron may serve as a proxy for dust when investigating the reduction of \gls{IO3-f}. In a series of \gls{CWFTRa} experiments, \citet{reza_iodine_2024} used a \gls{CE-DOASa} to detect \glssymbol{I2f}\ce{(g)} and a \gls{ToF I-CIMSa} to detect \glspl{OVOCa} associated with \gls{IO3-f} reduction in thin aqueous films. The films were inserted into the \gls{CWFTRa} and consisted of an organic or inorganic matrix and \gls{IO3-f}. + The organic matrices included \gls{IRON-3-CITRATEa}, \gls{CAa} and \gls{BTCAa}. \gls{CAa} was found in aerosol \citep{lienhard_measurements_2012} and is a proxy for oxygenated organic species. \gls{IRON-3-CITRATEa}, as a known photoactive compound, is considered a suitable proxy for \ce{Fe}(\toRoman{3}) carboxylate complexes found in the atmosphere \citep{reza_iodine_2024}. Importantly, \gls{CAa} has well-characterised hygroscopic properties \citep{reza_iodine_2024} so that this matrix can be used to control against \glspl{MATRIX-EFFECT-(CHEM)g} of organics that are due to iron when using \gls{IRON-3-CITRATEa}. These matrices were mixed with a solution of \gls{NaIO3f} to introduce \gls{IO3-f} at a concentration of $\approx\qty{30}{\milli\Molar}$. The results show that irradiation with \gls{VISa} for films containing \gls{IRON-3-CITRATEa} led to the reduction of $\approx\qty{40}{\percent}$ of the initially present \gls{IO3-f}. Likely, \gls{IRON-3-CITRATEa} undergoes a \gls{LMCTa} induced through irradiance with a photon at $\lambda<\qty{500}{\nano\meter}$ to yield \gls{CITRATEa} radicals and solvated electrons \ce{e-(aq)}, as described by \citet{saunders_insights_2012}. Likely, reduction of \gls{IO3-f} is driven through these solvated electrons. Furthermore, \citet{reza_iodine_2024} report that the speciation of the \glspl{CHROMOPHOREg} may include iodine-containing compounds. + +\end{document} \ No newline at end of file diff --git a/config/commands.tex b/config/commands.tex new file mode 100644 index 0000000..86e86ac --- /dev/null +++ b/config/commands.tex @@ -0,0 +1,5 @@ +%% CUSTOM MATH COMMANDS + +\newcommand{\der}[1]{\textnormal{d}{#1}} +\newcommand{\derf}[2]{\frac{\der{#1}}{\der{#2}}} +\newcommand{\RI}[1]{\ce{RI}_{{#1}}} diff --git a/config/glossary.tex b/config/glossary.tex new file mode 100644 index 0000000..acce426 --- /dev/null +++ b/config/glossary.tex @@ -0,0 +1,473 @@ +%% ------------------------------------------------------------------% +%% ACCRONYMS + +\newglossaryentry{CWFTRa}{ + type=\acronymtype, + first={coated wall flow tube reactor (CWFTR)\glsadd{CWFTRg}}, + name={CWFTR}, + description={Coated Wall Flow Tube Reactor}, + see=[see Glossary:]{CWFTRg} +} + +\newglossaryentry{vHPOa}{ + type=\acronymtype, + first={vanadium-dependent haloperoxidase (vHPO)}, + name={vHPO}, + description={Vanadium-dependent haloperoxidase} +} + +\newglossaryentry{IOPa}{ + type=\acronymtype, + first={iodine oxide particle (IOP)}, + firstplural={iodine oxide particles (IOPs)}, + name={IOP}, + description={Iodine oxide particle} +} + +\newglossaryentry{IUPACa}{ + type=\acronymtype, + first={International Union of Pure and Applied Chemistry (IUPAC)}, + name={IUPAC}, + description={International Union of Pure and Applied Chemistry} +} + +\newglossaryentry{UFAPa}{ + type=\acronymtype, + first={ultrafine aerosol particle (UFAP)}, + firstplural={ultrafine aerosol particles (UFAPs)}, + name={UFAP}, + description={ultrafine aerosol particle} +} + +\newglossaryentry{SOAa}{ + type=\acronymtype, + first={secondary organic aerosol (SOA)}, + name={SOA}, + description={secondary organic aerosol} +} + +\newglossaryentry{POAa}{ + type=\acronymtype, + first={primary organic aerosol (POA)}, + name={POA}, + description={primary organic aerosol} +} + +\newglossaryentry{OFRa}{ + type=\acronymtype, + first={oxidation flow reactor (OFR)}, + firstplural={oxidation flow reactors (OFRs)}, + name={OFR}, + description={oxidation flow reactor} +} + +\newglossaryentry{CCNa}{ + type=\acronymtype, + first={cloud condensation nucleus (CNN)}, + firstplural={cloud condensation nuclei (CNN)}, + name={CNN}, + description={cloud condensation nucleus} +} + +\newglossaryentry{DOASa}{ + type=\acronymtype, + first={differential optical absorbtion spectroscopy (DOAS)\glsadd{DOASg}}, + name={DOAS}, + description={Differential Optical Absorbtion Spectroscopy}, + see=[see Glossary:]{DOASg} +} + +\newglossaryentry{CE-DOASa}{ + type=\acronymtype, + first={cavity-enhanced differential optical absorbtion spectroscopy (CE-DOAS)\glsadd{CE-DOASg}}, + name={CE-DOAS}, + description={Cavity-Enhanced Differential Optical Absorbtion Spectroscopy}, + see=[see Glossary:]{CE-DOASg} +} + +\newglossaryentry{UV-Aa}{ + type=\acronymtype, + first={UV-A}, + name={UV-A}, + description={Ultraviolet-A light}, +} + +\newglossaryentry{UVa}{ + type=\acronymtype, + first={UV}, + name={UV}, + description={Ultraviolet light}, +} + +\newglossaryentry{VISa}{ + type=\acronymtype, + first={visible (VIS)}, + name={VIS}, + description={Visible light} +} + +\newglossaryentry{IRa}{ + type=\acronymtype, + first={infra red (IR)}, + name={IR}, + description={Infra red} +} + +\newglossaryentry{IRON-3-CITRATEa}{ + type=\acronymtype, + first={iron(\toRoman{3})-citrate}, + name={Fe-Cit}, + description={iron(\toRoman{3})-citrate} +} + +\newglossaryentry{CITRATEa}{ + type=\acronymtype, + first={citrate (Cit)}, + name={Cit}, + description={Citrate} +} + +\newglossaryentry{ATDa}{ + type=\acronymtype, + first={Arizona test dust (ATD)}, + name={ATD}, + description={Arizona test dust} +} + +\newglossaryentry{ABSa}{ + type=\acronymtype, + first={ammonium bisulfate (ABS) \glssymbol{ABSf}}, + name={ABS}, + description={Ammonium bisulfate} +} + +\newglossaryentry{CAa}{ + type=\acronymtype, + first={citric acid (CA)}, + name={CA}, + description={Citric acid} +} + +\newglossaryentry{BTCAa}{ + type=\acronymtype, + first={1,2,3,4 butanetetracarboxylic acid (BTCA)}, + name={BTCA}, + description={1,2,3,4 butanetetracarboxylic acid} +} + +\newglossaryentry{ALWa}{ + type=\acronymtype, + first={aerosol liquid water (ALW)\glsadd{ALWs}}, + name={ALW}, + description={Aerosol liquid water} +} + +\newglossaryentry{RHa}{ + type=\acronymtype, + first={relative humidity (RH)\glsadd{RHs}}, + name={RH}, + description={Relative humidity} +} + +\newglossaryentry{VOCa}{ + type=\acronymtype, + first={volatile organic compound (VOC)}, + firstplural={volatile organic compounds (VOCs)}, + name={VOC}, + description={Volatile Organic Compound} +} + +\newglossaryentry{VOICa}{ + type=\acronymtype, + first={volatile organic iodine compound (VOIC)\glsadd{RInf}}, + firstplural={volatile organic iodine compounds (VOICs)}, + name={VOIC}, + description={Volatile organic iodine compound} +} + +\newglossaryentry{OVOCa}{ + type=\acronymtype, + first={oxygenated volatile organic compound (OVOC)}, + firstplural={oxygenated volatile organic compounds (OVOCs)}, + name={OVOC}, + description={oxygenated volatile organic compound} +} + +\newglossaryentry{I-OVOCa}{ + type=\acronymtype, + first={iodine oxygenated volatile organic compound (I-OVOC)}, + firstplural={iodine oxygenated volatile organic compounds (I-OVOCs)}, + name={I-OVOC}, + description={iodine oxygenated volatile organic compound} +} + +\newglossaryentry{NDIRMa}{ + type=\acronymtype, + first={non-dispersive infrared monitor (NDIRM)}, + firstplural={non-dispersive infrared monitors (NDIRMs)}, + name={NDIRM}, + description={non-dispersive infrared monitor} +} + +\newglossaryentry{ToF CIMSa}{ + type=\acronymtype, + first={time-of-flight (ToF) chemical ionization mass spectrometer (CIMS) (ToF I-CIMS)}, + firstplural={time-of-flight (ToF) chemical ionization mass spectrometers (CIMSs) (ToF I-CIMSs)}, + name={ToF CIMS}, + description={time-of-flight chemical ionization mass spectrometer} +} + +\newglossaryentry{PSIa}{ + type=\acronymtype, + first={Paul-Scherrer Institute (PSI)}, + name={PSI}, + description={Paul-Scherrer Institute} +} + +\newglossaryentry{LMCTa}{ + type=\acronymtype, + first={ligand-to-metal charge transfer (LMCT)}, + name={LMCT}, + description={Bla Bla bla} +} + +\newglossaryentry{ROSa}{ + type=\acronymtype, + first={reactive oxygen species (ROS)\glsadd{ROSg}}, + name={ROS}, + see=[see Glossary:]{ROSg}, + description={Bla Bla bla} +} + +\newglossaryentry{BRAY-LIEBHAFSKY-MECHANISMa}{ + type=\acronymtype, + first={Bray-Liebhafsky mechanism (BLM)\glsadd{BRAY-LIEBHAFSKY-MECHANISMg}}, + name={BLM}, + see=[see Glossary:]{BRAY-LIEBHAFSKY-MECHANISMg}, + description={Bla Bla bla} +} + +\newglossaryentry{BRIGGS-RAUSCHER-MECHANISMa}{ + type=\acronymtype, + first={Briggs-Rauscher mechanism (BRM)\glsadd{BRIGGS-RAUSCHER-MECHANISMg}}, + name={BRM}, + see=[see Glossary:]{BRIGGS-RAUSCHER-MECHANISMg}, + description={Bla Bla bla} +} + +\newglossaryentry{LE-CHATELIER-PRINCIPLEa}{ + type=\acronymtype, + first={Le Chatelier's principle (LCP)\glsadd{LE-CHATELIER-PRINCIPLEg}}, + name={LCP}, + see=[see Glossary:]{LE-CHATELIER-PRINCIPLEg}, + description={Bla Bla bla} +} + +\newglossaryentry{SOIa}{ + type=\acronymtype, + first={soluble organic iodine (SOI)}, + name={SOI}, + description={Soluble organic iodine} +} + +\newglossaryentry{RISa}{ + type=\acronymtype, + first={reactive iodine species (RIS)}, + name={RIS}, + description={Reactive Iodine Species} +} + +\newglossaryentry{HAa}{ + type=\acronymtype, + first={humic acid (HA)}, + name={HA}, + description={Humic acid} +} + +\newglossaryentry{HOMa}{ + type=\acronymtype, + first={highly oxidised organic molecule (HOM)}, + firstplural={highly oxidised organic molecules (HOMs)}, + name={HOM}, + description={Highly oxidised organic molecule} +} + +%% ------------------------------------------------------------------% +%% GLOSSARY ENTRIES + +\newglossaryentry{DIFFUSIONg}{ + text={diffusion}, + name={diffusion}, + description={Blablabla}, + sort={diffusion}, + user1={diffusion}, + type=main, + category=main +} + + \newglossaryentry{MOLECULAR-DIFFUSIONg}{ + text={molecular diffusion}, + name={molecular diffusion}, + parent={DIFFUSIONg}, + description={An imbalance between free radicals and antioxidants, leading to damage to the organism through the oxidation of the radicals with non-antioxidant tissue.}, + sort={Diffusion!molecular}, + user1={molecular}, + type=main, + category=main + } + + \newglossaryentry{EDDY-DIFFUSIONg}{ + text={eddy diffusion}, + name={eddy diffusion}, + parent={DIFFUSIONg}, + description={An imbalance between free radicals and antioxidants, leading to damage to the organism through the oxidation of the radicals with non-antioxidant tissue.}, + sort={Diffusion!eddy}, + user1={eddy}, + type=main, + category=main + } + +\newglossaryentry{DOASg}{ + first={differential optical absorption spectroscopy (DOAS)}, + text={DOAS}, + name={DOAS}, + short={DOAS}, + description={Description}, + sort={Spectroscopy!differential optical absorption}, + user1={differential optical absorbtion}, + type=main, + category=main +} + + \newglossaryentry{CE-DOASg}{ + text={CE-DOAS}, + name={CE-DOAS}, + parent={DOASg}, + see={DOASg}, + description={Bla}, + sort={Spectroscopy!differential optical absorbtion!cavity-enhanced}, + user1={cavity-enhanced}, + type=main, + category=main + } + +\newglossaryentry{MATRIX-(CHEM)g}{ + first={matrix\glsadd{MATRIX-EFFECT-(CHEM)g}}, + firstplural={matrices\glsadd{MATRIX-EFFECT-(CHEM)g}}, + text={matrix}, + name={Matrix (chem.)}, + plural={matrices}, + description={The components of a solution that are not specifically alanysed but that may significantly alter the behaviour of the substance to be analysed, for instance through matrix effects.}, + see={MATRIX-EFFECT-(CHEM)g}, + sort={matrix}, + user1={film}, + type=main, + category=main +} + + \newglossaryentry{MATRIX-EFFECT-(CHEM)g}{ + text={matrix effect}, + name={matrix effect}, + parent={MATRIX-(CHEM)g}, + plural={matrix effects}, + description={The effect that matrix has on the analysis and its outcome}, + sort={matrix!effect}, + user1={effect}, + type=main, + category=main + } + +\newglossaryentry{CWFTRg}{ + first={coated wall flow tube reactor (CWFTR)}, + firstplural={coated wall flow tube reactors (CWFRTs)}, + text={CWFTR}, + name={CWFTR}, + description={blabla}, + sort={coated wall flow tube}, + user1={coated wall flow tube}, + type=main, + category=main +} + +\newglossaryentry{CHROMOPHOREg}{ + text={chromophore}, + plural={chromophores}, + name={Chromophore}, + description={Describtoip}, + sort={chromophore}, + user1={Chromophore}, + type=main, + category=main +} + +\newglossaryentry{ACTINIC-FLUXg}{ + text={actinic flux}, + plural={actinic fluxes}, + name={Actinic flux}, + description={Bla bla bla}, + sort={Actinic Flux}, + user1={Actinic}, + type=main, + category=main +} + +\newglossaryentry{OXIDATIBVE-STRESSg}{ + text={oxidative stress}, + name={Oxidative stress}, + description={An imbalance between free radicals and antioxidants, leading to damage to the organism through the oxidation of the radicals with non-antioxidant tissue.}, + sort={Oxidative!stress}, + user1={stress}, + type=main, + category=main +} + +\newglossaryentry{ROSg}{ + text={ROS}, + name={ROS}, + description={Bla bla bla}, + sort={ROS}, + user1={ROS}, + type=main, + category=main +} + +\newglossaryentry{FENTON-CYCLEg}{ + text={fenton cycle}, + name={Fenton cylce}, + description={Bla bla bla}, + sort={fenton cycle}, + user1={fenton cycle}, + type=main, + category=main +} + +\newglossaryentry{BRAY-LIEBHAFSKY-MECHANISMg}{ + text={Bray-Liebhafsky mechanism}, + name={Bray-Liebhafsky mechanism}, + description={Bla bla bla}, + sort={Bray-Liebhafsky mechanism}, + user1={Bray-Liebhafsky mechanism}, + type=main, + category=main +} + +\newglossaryentry{BRIGGS-RAUSCHER-MECHANISMg}{ + text={Briggs-Rauscher mechanism}, + name={Briggs-Rauscher mechanism}, + description={Bla bla bla}, + sort={Briggs-Rauscher mechanism}, + user1={Briggs-Rauscher mechanism}, + type=main, + category=main +} + +\newglossaryentry{LE-CHATELIER-PRINCIPLEg}{ + text={Le Chatelier's principle}, + first={Le Chatelier's principle (LCP)}, + name={Le Chatelier's principle (LCP)}, + description={Bla bla bla}, + sort={Le Chatelier's principle}, + user1={Le Chatelier's principle}, + type=main, + category=main +} \ No newline at end of file diff --git a/config/literature.bib b/config/literature.bib new file mode 100644 index 0000000..f002d94 --- /dev/null +++ b/config/literature.bib @@ -0,0 +1,2420 @@ + +@incollection{carpenter_biogeochemical_2015, + edition = {2}, + title = {Biogeochemical Cycles - Iodine}, + rights = {https://www.elsevier.com/tdm/userlicense/1.0/}, + isbn = {978-0-12-382225-3}, + url = {https://linkinghub.elsevier.com/retrieve/pii/B9780123822253004850}, + pages = {205--219}, + booktitle = {Encyclopedia of Atmospheric Sciences}, + publisher = {Elsevier}, + author = {Carpenter, L.J.}, + urldate = {2025-01-24}, + date = {2015}, + langid = {english}, + doi = {10.1016/B978-0-12-382225-3.00485-0}, + keywords = {Review, Unread}, + file = {PDF:/Users/davidtschan/Zotero/storage/IJU3SUSM/Carpenter - 2015 - BIOGEOCHEMICAL CYCLES Iodine.pdf:application/pdf}, +} + +@article{saiz-lopez_reactive_2012, + title = {Reactive halogen chemistry in the troposphere}, + volume = {41}, + issn = {0306-0012, 1460-4744}, + url = {https://xlink.rsc.org/?DOI=c2cs35208g}, + doi = {10.1039/c2cs35208g}, + pages = {6448}, + number = {19}, + journaltitle = {Chemical Society Reviews}, + shortjournal = {Chem. Soc. Rev.}, + author = {Saiz-Lopez, Alfonso and Von Glasow, Roland}, + urldate = {2025-01-24}, + date = {2012}, + langid = {english}, + keywords = {Review, Unread}, + file = {PDF:/Users/davidtschan/Zotero/storage/HDNREBXV/Saiz-Lopez and Von Glasow - 2012 - Reactive halogen chemistry in the troposphere.pdf:application/pdf}, +} + +@article{saiz-lopez_atmospheric_2012, + title = {Atmospheric Chemistry of Iodine}, + volume = {112}, + issn = {0009-2665, 1520-6890}, + url = {https://pubs.acs.org/doi/10.1021/cr200029u}, + doi = {10.1021/cr200029u}, + pages = {1773--1804}, + number = {3}, + journaltitle = {Chemical Reviews}, + shortjournal = {Chem. Rev.}, + author = {Saiz-Lopez, Alfonso and Plane, John M. C. and Baker, Alex R. and Carpenter, Lucy J. and Von Glasow, Roland and Gómez Martín, Juan C. and {McFiggans}, Gordon and Saunders, Russell W.}, + urldate = {2025-01-24}, + date = {2012-03-14}, + langid = {english}, + keywords = {Review, Unread}, + file = {PDF:/Users/davidtschan/Zotero/storage/VIRXISNG/Saiz-Lopez et al. - 2012 - Atmospheric Chemistry of Iodine.pdf:application/pdf}, +} + +@article{toda_isolation_2011, + title = {Isolation and characterization of a gene encoding a \textit{S}-adenosyl-l-methionine-dependent halide/thiol methyltransferase ({HTMT}) from the marine diatom \textit{Phaeodactylum tricornutum}: Biogenic mechanism of {CH}3I emissions in oceans}, + volume = {72}, + issn = {0031-9422}, + url = {https://www.sciencedirect.com/science/article/pii/S003194221000467X}, + doi = {10.1016/j.phytochem.2010.12.003}, + shorttitle = {Isolation and characterization of a gene encoding a \textit{S}-adenosyl-l-methionine-dependent halide/thiol methyltransferase ({HTMT}) from the marine diatom \textit{Phaeodactylum tricornutum}}, + abstract = {Several marine algae including diatoms exhibit S-adenosyl-l-methionine ({SAM}) halide/thiol methyltransferase ({HTMT}) activity, which is involved in the emission of methyl halides. In this study, the in vivo biogenic emission of methyl iodide from the diatom Phaeodactylum tricornutum was found to be clearly correlated with iodide concentration in the incubation media. The gene encoding {HTMT} (Pthtmt) was isolated from P. tricornutum {CCAP} 1055/1, and expressed in Escherichia coli. The molecular weight of the enzyme was 29.7kDa including a histidine tag, and the optimal {pH} was around {pH} 7.0. The kinetic properties of recombinant {PtHTMT} towards Cl−, Br−, I−, [{SH}]−, [{SCN}]−, and {SAM} were 637.88mM, 72.83mM, 8.60mM, 9.92mM, 7.9mM, and 0.016mM, respectively, and were similar to those of higher-plant {HTMTs}, except that the activity towards thiocyanate was lower. The biogenic emission of methyl halides from the cultured cells and the enzymatic properties of {HTMT} suggest that the {HMT}/{HTMT} reaction is key to understanding the biogenesis of methyl halides in oceanic environments as well as terrestrial ones.}, + pages = {337--343}, + number = {4}, + journaltitle = {Phytochemistry}, + shortjournal = {Phytochemistry}, + author = {Toda, Hiroshi and Itoh, Nobuya}, + urldate = {2025-03-28}, + date = {2011-04-01}, + keywords = {-Adenosyl--methionine ({SAM}): halide/thiol methyltransferase, Methyl halides, Methyl iodide}, + file = {PDF:/Users/davidtschan/Zotero/storage/7HR4Y6FR/Toda and Itoh - 2011 - Isolation and characterization of a gene encoding a S-adenosyl-l-methionine-dependent halide.pdf:application/pdf;ScienceDirect Snapshot:/Users/davidtschan/Zotero/storage/LJY39S5Z/S003194221000467X.html:text/html}, +} + +@article{amachi_microbial_2008, + title = {Microbial contribution to global iodine cycling: Volatilization, accumulation, reduction, oxidation, and sorption of iodine}, + volume = {23}, + doi = {10.1264/jsme2.ME08548}, + shorttitle = {Microbial contribution to global iodine cycling}, + abstract = {Iodine is an essential trace element for humans and animals because of its important role as a constituent of thyroid hormones. If the anthropogenic iodine-129 (129I, half-life: 1.6x107 years), which is released from nuclear facilities into the environment and has a long half-life, participates in the biogeochemical cycling of iodine, it potentially accumulates in the human thyroid gland and might cause thyroid cancer. Therefore, it is necessary to obtain better information on the behavior of iodine in the environment for accurate safety assessments of 129I. Major pathways of iodine cycling are the volatilization of organic iodine compounds into the atmosphere, accumulation of iodine in living organisms, oxidation and reduction of inorganic iodine species, and sorption of iodine by soils and sediments. Considerable geochemical evidence has indicated that these processes are influenced or controlled by microbial activities, although the precise mechanisms involved are still unclear. This review summarizes current knowledge on interactions between microorganisms and iodine, with special emphasis on newly isolated bacteria possibly contributing to the cycling of iodine on a global scale.}, + pages = {269--276}, + number = {4}, + journaltitle = {Microbes and Environments}, + author = {Amachi, S.}, + date = {2008}, + keywords = {Biogeochemical cycling, Iodine, Microorganisms, Ozone destruction, Radionuclide}, + file = {Full Text:/Users/davidtschan/Zotero/storage/J8RZ6XKB/Amachi - 2008 - Microbial contribution to global iodine cycling Volatilization, accumulation, reduction, oxidation,.pdf:application/pdf;Snapshot:/Users/davidtschan/Zotero/storage/MCCRCX8T/display.html:text/html}, +} + +@article{muramatsu_studies_2004, + title = {Studies with natural and anthropogenic iodine isotopes: iodine distribution and cycling in the global environment}, + volume = {74}, + issn = {0265-931X}, + url = {https://www.sciencedirect.com/science/article/pii/S0265931X04000165}, + doi = {10.1016/j.jenvrad.2004.01.011}, + series = {Papers from the International Conference on Radioactivity in the Environment, Monaco, 1-5 September 2002}, + shorttitle = {Studies with natural and anthropogenic iodine isotopes}, + abstract = {Iodine is an important trace element in geological and biological processes. We summarize here recent results and new data of experiments and observations carried out to improve the understanding of concentration levels and behavior of natural and anthropogenic iodine nuclides in the global environment. The distribution of stable iodine in the Earth’s crust was estimated using concentration data in a suite of representative samples and the influence of subduction on the marine iodine cycle was investigated using 129I systematics on iodine-rich brines from Japan. The importance of microorganisms for the natural iodine cycle is shown in recent studies of iodine sorption on soil and of iodine volatilization from terrestrial and marine environments. Levels of anthropogenic 129I were measured in samples collected around a spent fuel reprocessing plant in Japan.}, + pages = {221--232}, + number = {1}, + journaltitle = {Journal of Environmental Radioactivity}, + shortjournal = {Journal of Environmental Radioactivity}, + author = {Muramatsu, Yasuyuki and Yoshida, Satoshi and Fehn, Udo and Amachi, Seigo and Ohmomo, Yoichiro}, + urldate = {2025-04-16}, + date = {2004-01-01}, + keywords = {Iodine, Crust, Iodine-129, Microbial activities, Soil}, + file = {PDF:/Users/davidtschan/Zotero/storage/5ECXTQ69/Muramatsu et al. - 2004 - Studies with natural and anthropogenic iodine isotopes iodine distribution and cycling in the globa.pdf:application/pdf;ScienceDirect Snapshot:/Users/davidtschan/Zotero/storage/SXX2R9WV/S0265931X04000165.html:text/html}, +} + +@article{whitehead_distribution_1984, + title = {The distribution and transformations of iodine in the environment}, + volume = {10}, + issn = {0160-4120}, + url = {https://www.sciencedirect.com/science/article/pii/0160412084901399}, + doi = {10.1016/0160-4120(84)90139-9}, + abstract = {Iodine in the atmosphere is derived largely from seawater. It is probable that the biological production of methyl iodide is important in this transfer. Subsequent photolytic dissociation and oxidation of the methyl iodide, together with other inputs, with partial sorption of the products by aerosols, results in the atmospheric iodine being distributed between various gaseous and particulate forms. Atmospheric iodine is the major source of the iodine in soils, and the process of enrichment continues throughout soil formation and development until ultimately an equilibrium concentration is attained. The retention of iodine in soils is due mainly to the organic matter and hydrous oxides of iron and aluminum. In humid areas, only small proportions of the total soil iodine are soluble in water or available for uptake by plants. The atmosphere is also a direct source of iodine for plants, and in some situations may be more important than the soil. Iodine may be lost from soils by leaching, volatilization, and removal in crops, but the magnitude of these processes is difficult to assess. However, the amounts of iodine reported in groundwaters, and in rivers and lakes remote from human activity, suggest that some leaching of iodine is widespread. Increased amounts of iodine occur in rivers receiving effluent from sewage works. Milk and milk products are now major dietary sources of iodine because their content is often increased by concentrate feedingstuffs supplemented with iodine and/or by the use in dairies of iodophor detergents and sterilants.}, + pages = {321--339}, + number = {4}, + journaltitle = {Environment International}, + shortjournal = {Environment International}, + author = {Whitehead, D. C.}, + urldate = {2025-04-16}, + date = {1984-01-01}, + file = {PDF:/Users/davidtschan/Zotero/storage/EHJ5H87E/Whitehead - 1984 - The distribution and transformations of iodine in the environment.pdf:application/pdf;ScienceDirect Snapshot:/Users/davidtschan/Zotero/storage/Y8NPVYPG/0160412084901399.html:text/html}, +} + +@article{winter_exploring_2009, + title = {Exploring the Chemistry and Biology of Vanadium-dependent Haloperoxidases*}, + volume = {284}, + issn = {0021-9258}, + url = {https://www.sciencedirect.com/science/article/pii/S0021925819811894}, + doi = {10.1074/jbc.R109.001602}, + abstract = {Nature has developed an exquisite array of methods to introduce halogen atoms into organic compounds. Most of these enzymes are oxidative and require either hydrogen peroxide or molecular oxygen as a cosubstrate to generate a reactive halogen atom for catalysis. Vanadium-dependent haloperoxidases contain a vanadate prosthetic group and utilize hydrogen peroxide to oxidize a halide ion into a reactive electrophilic intermediate. These metalloenzymes have a large distribution in nature, where they are present in macroalgae, fungi, and bacteria, but have been exclusively characterized in eukaryotes. In this minireview, we highlight the chemistry and biology of vanadium-dependent haloperoxidases from fungi and marine algae and the emergence of new bacterial members that extend the biological function of these poorly understood halogenating enzymes.}, + pages = {18577--18581}, + number = {28}, + journaltitle = {Journal of Biological Chemistry}, + shortjournal = {Journal of Biological Chemistry}, + author = {Winter, Jaclyn M. and Moore, Bradley S.}, + urldate = {2025-04-16}, + date = {2009-07-10}, + file = {Full Text:/Users/davidtschan/Zotero/storage/SCIPRF8V/Winter and Moore - 2009 - Exploring the Chemistry and Biology of Vanadium-dependent Haloperoxidases.pdf:application/pdf;ScienceDirect Snapshot:/Users/davidtschan/Zotero/storage/R445QLIF/S0021925819811894.html:text/html}, +} + +@article{kupper_iodide_2008, + title = {Iodide accumulation provides kelp with an inorganic antioxidant impacting atmospheric chemistry}, + volume = {105}, + url = {https://www.pnas.org/doi/full/10.1073/pnas.0709959105}, + doi = {10.1073/pnas.0709959105}, + abstract = {Brown algae of the Laminariales (kelps) are the strongest accumulators of iodine among living organisms. They represent a major pump in the global biogeochemical cycle of iodine and, in particular, the major source of iodocarbons in the coastal atmosphere. Nevertheless, the chemical state and biological significance of accumulated iodine have remained unknown to this date. Using x-ray absorption spectroscopy, we show that the accumulated form is iodide, which readily scavenges a variety of reactive oxygen species ({ROS}). We propose here that its biological role is that of an inorganic antioxidant, the first to be described in a living system. Upon oxidative stress, iodide is effluxed. On the thallus surface and in the apoplast, iodide detoxifies both aqueous oxidants and ozone, the latter resulting in the release of high levels of molecular iodine and the consequent formation of hygroscopic iodine oxides leading to particles, which are precursors to cloud condensation nuclei. In a complementary set of experiments using a heterologous system, iodide was found to effectively scavenge {ROS} in human blood cells.}, + pages = {6954--6958}, + number = {19}, + journaltitle = {Proceedings of the National Academy of Sciences}, + author = {Küpper, Frithjof C. and Carpenter, Lucy J. and {McFiggans}, Gordon B. and Palmer, Carl J. and Waite, Tim J. and Boneberg, Eva-Maria and Woitsch, Sonja and Weiller, Markus and Abela, Rafael and Grolimund, Daniel and Potin, Philippe and Butler, Alison and Luther, George W. and Kroneck, Peter M. H. and Meyer-Klaucke, Wolfram and Feiters, Martin C.}, + urldate = {2025-04-17}, + date = {2008-05-13}, + note = {Publisher: Proceedings of the National Academy of Sciences}, + file = {0709959105si:/Users/davidtschan/Zotero/storage/PRNZ53MF/0709959105si.pdf:application/pdf;Full Text PDF:/Users/davidtschan/Zotero/storage/HVTNZN6G/Küpper et al. - 2008 - Iodide accumulation provides kelp with an inorganic antioxidant impacting atmospheric chemistry.pdf:application/pdf}, +} + +@article{carrano_influence_2020, + title = {The influence of marine algae on iodine speciation in the coastal ocean}, + volume = {35}, + issn = {1226-2617, 2093-0860}, + url = {http://e-algae.org/journal/view.php?doi=10.4490/algae.2020.35.5.25}, + doi = {10.4490/algae.2020.35.5.25}, + pages = {167--176}, + number = {2}, + journaltitle = {Algae}, + shortjournal = {Algae}, + author = {Carrano, Mary W. and Yarimizu, Kyoko and Gonzales, Jennifer L. and Cruz-López, Ricardo and Edwards, Matthew S. and Tymon, Teresa M. and Küpper, Frithjof C. and Carrano, Carl J. and Carrano, Mary W. and Yarimizu, Kyoko and Gonzales, Jennifer L. and Cruz-López, Ricardo and Edwards, Matthew S. and Tymon, Teresa M. and Küpper, Frithjof C. and Carrano, Carl J.}, + urldate = {2025-04-17}, + date = {2020-06-15}, + note = {Publisher: The Korean Society of Phycology}, + file = {algae-2020-35-5-25:/Users/davidtschan/Zotero/storage/5KYYM7VC/algae-2020-35-5-25.pdf:application/pdf;Full Text PDF:/Users/davidtschan/Zotero/storage/JQKXH2PC/Carrano et al. - 2020 - The influence of marine algae on iodine speciation in the coastal ocean.pdf:application/pdf}, +} + +@article{palmer_iodine_2005, + title = {Iodine and Halocarbon Response of Laminaria digitata to Oxidative Stress and Links to Atmospheric New Particle Production}, + volume = {2}, + issn = {1449-8979}, + url = {https://www.publish.csiro.au/en/EN05078}, + doi = {10.1071/EN05078}, + abstract = {Environmental Context.Various organic iodine compounds (including {CH}3I, {CH}2ClI, {CH}2BrI, {CH}2I2) are present throughout the marine boundary layer as a result of their production from seaweeds, phytoplankton, and photolysis reactions occurring in seawater. In air, these compounds rapidly photolyse to give atomic I which subsequently reacts with ozone to form iodine oxide, potentially leading to perturbations of the tropospheric oxidative capacity and nucleation of atmospheric particles. Recent research has identified molecular iodine as an additional source of iodine atoms to coastal areas. Here we study the relative roles and controls of gaseous organic and molecular iodine release from the seaweed Laminaria digitata. Abstract.Changes in the halocarbon, I2 and particle production of the brown algal kelp Laminaria digitata as a response to different chemical stresses have been investigated. Oxidative stress (caused by either exogenous hydrogen peroxide, gaseous ozone or a solution of oligoguluronates, known elicitors of oxidative stress) caused increased halocarbon and I2 production by the seaweed. The maximum I2 release was observed under exposure to O3 (at several hundred parts per billion by volume (ppbv)), whereas oligoguluronates elicited the highest release of iodine-containing halocarbons including {CH}2I2. Significantly greater production of I2, compared to {CH}2I2, was observed at atmospheric levels of ozone. Particle production was observed only when the Laminaria samples were exposed to ozone (up to 16 000 cm−3 s−1 per gram fresh weight ({FW}) of seaweed with a {\textasciitilde}2 min residence time and with a total I atom flux of 1.6 × 108 cm−3 s−1 g−1 {FW} from photolysis of I2); passing O3-free air over the unstressed seaweed followed by secondary mixing with ozone did not result in any measurable particle formation. Our limited data indicate that ozone elicits abiotic production of I2 from Laminaria and that there is a direct relationship between the amount of I2 released and the number of particles formed. The results support the recent hypothesis that molecular iodine rather than volatile organic iodine (e.g. {CH}2I2) release from exposed seaweeds is the major source of coastal new particle production.}, + pages = {282--290}, + number = {4}, + journaltitle = {Environmental Chemistry}, + shortjournal = {Environ. Chem.}, + author = {Palmer, Carl J. and Anders, Thorsten L. and Carpenter, Lucy J. and Küpper, Frithjof C. and {McFiggans}, Gordon B.}, + urldate = {2025-04-17}, + date = {2005-12-08}, + langid = {english}, + note = {Publisher: {CSIRO} {PUBLISHING}}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/EX548532/Palmer et al. - 2005 - Iodine and Halocarbon Response of Laminaria digitata to Oxidative Stress and Links to Atmospheric Ne.pdf:application/pdf}, +} + +@article{liu_kinetics_2001, + title = {Kinetics and Mechanisms of Aqueous Ozone Reactions with Bromide, Sulfite, Hydrogen Sulfite, Iodide, and Nitrite Ions}, + volume = {40}, + issn = {0020-1669}, + url = {https://doi.org/10.1021/ic000919j}, + doi = {10.1021/ic000919j}, + abstract = {Reactions of ozone with Br-, {SO}32-, {HSO}3-, I-, and {NO}2-, studied by stopped-flow and pulsed-accelerated-flow techniques, are first order in the concentration of O3(aq) and first order in the concentration of each anion. The rate constants increase by a factor of 5 × 106 as the nucleophilicities of the anions increase from Br- to {SO}32-. Ozone adducts with the nucleophiles are proposed as steady-state intermediates prior to oxygen atom transfer with release of O2. Ab initio calculations show possible structures for the intermediates. The reaction between Br- and O3 is accelerated by H+ but exhibits a kinetic saturation effect as the acidity increases. The kinetics indicate formation of {BrOOO}- as a steady-state intermediate with an acid-assisted step to give {BrOH} and O2. Temperature dependencies of the reactions of Br- and {HSO}3- with O3 in acidic solutions are determined from 1 to 25 °C. These kinetics are important in studies of annual ozone depletion in the Arctic troposphere at polar sunrise.}, + pages = {4436--4442}, + number = {17}, + journaltitle = {Inorganic Chemistry}, + shortjournal = {Inorg. Chem.}, + author = {Liu, Qian and Schurter, Lynn M. and Muller, Charles E. and Aloisio, Simone and Francisco, Joseph S. and Margerum, Dale W.}, + urldate = {2025-04-18}, + date = {2001-08-01}, + note = {Publisher: American Chemical Society}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/NMYRCWB8/Liu et al. - 2001 - Kinetics and Mechanisms of Aqueous Ozone Reactions with Bromide, Sulfite, Hydrogen Sulfite, Iodide,.pdf:application/pdf}, +} + +@article{fuge_iodine_2015, + title = {Iodine and human health, the role of environmental geochemistry and diet, a review}, + volume = {63}, + issn = {0883-2927}, + url = {https://www.sciencedirect.com/science/article/pii/S0883292715300470}, + doi = {10.1016/j.apgeochem.2015.09.013}, + abstract = {Iodine is an essential element in the human diet and a deficiency can lead to a number of health outcomes collectively termed iodine deficiency disorders ({IDD}). The geochemistry of iodine is dominated by its volatility with volatilisation of organo-iodine compounds and elemental iodine from biological and non-biological sources in the oceans being a major component of its global cycle. As a result of the dominant oceanic source, iodine is strongly enriched in near-coastal soils, however, the major zone of marine influence generally stretches to only 50–80 km inland and terrestrial sources of volatilised iodine, from wetlands, soils and plants are also an important aspect of its global geochemical cycle. Iodine in soils is strongly bound with transfer factors from soil to plants being generally small and as a consequence there is only limited uptake of iodine through the plant root system. It is likely that uptake of atmospheric iodine by the aerial parts of plants is an essential process and, along with iodine deposited on plant surfaces, is a major source for grazing animals. Human intake of iodine is mainly from food with some populations also obtaining appreciable quantities of iodine from drinking water. Plant-derived dietary iodine is generally insufficient as evidenced from the low dietary iodine of strict vegan diets. Seafood provides major iodine-rich dietary items but other inputs are mainly from adventitious sources, such as the use of iodised salt and from dairy produce, which is a rich source mainly due to cattle-feed being fortified with iodine, and to the use of iodine-containing sterilants in the dairy industry. While the distribution and geochemistry of iodine are reflected in the global distribution of {IDD}, the recent upsurge of {IDD} in developed countries would seem to reflect changes in diet.}, + pages = {282--302}, + journaltitle = {Applied Geochemistry}, + shortjournal = {Applied Geochemistry}, + author = {Fuge, Ron and Johnson, Christopher C.}, + urldate = {2025-04-22}, + date = {2015-12-01}, + keywords = {Iodine, Dietary iodine, Global cycling, Iodine deficiency disorders ({IDD}), Organo-iodine, Volatilisation}, + file = {PDF:/Users/davidtschan/Zotero/storage/8T9UK8C4/Fuge and Johnson - 2015 - Iodine and human health, the role of environmental geochemistry and diet, a review.pdf:application/pdf;ScienceDirect Snapshot:/Users/davidtschan/Zotero/storage/X2WILILB/S0883292715300470.html:text/html}, +} + +@article{moreda-pineiro_review_2011, + title = {A review on iodine speciation for environmental, biological and nutrition fields}, + volume = {26}, + issn = {0267-9477}, + url = {http://dx.doi.org/10.1039/C0JA00272K}, + doi = {10.1039/C0JA00272K}, + abstract = {A review of recent literature focused on iodine determination/speciation in environmental, biological and clinical materials is provided. The review covers the different sample pre-treatments to extract total iodine, as well as specific iodinated forms, and the most used analytical techniques for assessing total iodine (cathodic stripping voltammetry, differential pulse voltammetry, neutron activation analysis, catalytic spectrophotometry, and atomic spectrometric techniques, mainly inductively coupled plasma-mass spectrometry) and iodine speciation (nonchromatographic methods, and mainly high performance liquid chromatography, gas chromatography and capillary electrophoresis coupled to electrochemical, {UV} spectrophotometric and mass spectrometric detection).}, + pages = {2107--2152}, + number = {11}, + journaltitle = {Journal of Analytical Atomic Spectrometry}, + shortjournal = {J. Anal. At. Spectrom.}, + author = {Moreda-Piñeiro, Antonio and Romarís-Hortas, Vanessa and Bermejo-Barrera, Pilar}, + date = {2011}, + note = {Publisher: The Royal Society of Chemistry}, + file = {PDF:/Users/davidtschan/Zotero/storage/YI8HD6RY/Moreda-Piñeiro et al. - 2011 - A review on iodine speciation for environmental, biological and nutrition fields.pdf:application/pdf}, +} + +@article{kendrick_halogen_2024, + title = {Halogen Cycling in the Solid Earth}, + volume = {52}, + issn = {0084-6597, 1545-4495}, + url = {https://www.annualreviews.org/content/journals/10.1146/annurev-earth-031621-111700}, + doi = {10.1146/annurev-earth-031621-111700}, + abstract = {Each of the halogens constrains a different aspect of volatile cycling in the solid Earth. F is moderately incompatible in the mantle and has a low mobility at Earth\'s surface, meaning that it is preferentially retained in the mantle and continental crust. In contrast, Cl, Br, and I are strongly incompatible and highly soluble. Chloride is the dominant anion in seawater and many geofluids and a major component of evaporite minerals. Br and I are essential for life and significantly incorporated into organic matter that accumulates in marine sediments. Surficial fluids circulated into continental and oceanic crust incorporate surface-derived halogens into alteration minerals. As a result, subducting slabs and arc lavas are weakly enriched in F and strongly enriched in Cl, Br, and I. Subduction has maintained mantle Cl and Br concentrations at relatively constant levels since Earth\'s early differentiation, but mantle I/Cl has decreased over time. ▪ Halogen abundances on the early Earth were affected by I partitioning into Earth\'s core and possible loss of hydrophilic Cl, Br, and I in an early formed ocean. ▪ Halogens are powerful tracers of subduction zone processes on the modern Earth, with Cl, Br, and I having a dominantly subducted origin in Earth\'s mantle. ▪ The deep subduction cycles of Cl, Br, and I are more similar to that of H2O than they are to F, but the geochemical cycle of each halogen differs in detail. ▪ Halogen abundance ratios and stable isotope ratios vary systematically in Earth\'s surface reservoirs, meaning that halogens are powerful tracers of geological fluids and melts.}, + pages = {195--220}, + issue = {Volume 52, 2024}, + journaltitle = {Annual Review of Earth and Planetary Sciences}, + author = {Kendrick, Mark A.}, + urldate = {2025-04-24}, + date = {2024-07-23}, + langid = {english}, + note = {Publisher: Annual Reviews}, + keywords = {iodine cycle, Reading}, + file = {PDF:/Users/davidtschan/Zotero/storage/TQDQG2NU/Kendrick - 2024 - Halogen Cycling in the Solid Earth.pdf:application/pdf;Snapshot:/Users/davidtschan/Zotero/storage/W7UXH9FN/annurev-earth-031621-111700.html:text/html}, +} + +@article{enami_global_2007, + title = {Global Inorganic Source of Atmospheric Bromine}, + volume = {111}, + issn = {1089-5639}, + url = {https://doi.org/10.1021/jp074903r}, + doi = {10.1021/jp074903r}, + abstract = {A few bromine molecules per trillion (ppt) causes the complete destruction of ozone in the lower troposphere during polar spring and about half of the losses associated with the “ozone hole” in the stratosphere. Recent field and aerial measurements of the proxy {BrO} in the free troposphere suggest an even more pervasive global role for bromine. Models, which quantify ozone trends by assuming atmospheric inorganic bromine (Bry) stems exclusively from long-lived bromoalkane gases, significantly underpredict {BrO} measurements. This discrepancy effectively implies a ubiquitous tropospheric background level of ∼4 ppt Bry of unknown origin. Here, we report that I- efficiently catalyzes the oxidation of Br- and Cl- in aqueous nanodroplets exposed to ozone, the everpresent atmospheric oxidizer, under conditions resembling those encountered in marine aerosols. Br- and Cl-, which are rather unreactive toward O3 and were previously deemed unlikely direct precursors of atmospheric halogens, are readily converted into {IBr}2- and {ICl}2- en route to Br2(g) and Cl2(g) in the presence of I-. Fine sea salt aerosol particles, which are predictably and demonstrably enriched in I- and Br-, are thus expected to globally release photoactive halogen compounds into the atmosphere, even in the absence of sunlight.}, + pages = {8749--8752}, + number = {36}, + journaltitle = {The Journal of Physical Chemistry A}, + shortjournal = {J. Phys. Chem. A}, + author = {Enami, S. and Vecitis, C. D. and Cheng, J. and Hoffmann, M. R. and Colussi, A. J.}, + urldate = {2025-04-29}, + date = {2007-09-01}, + note = {Publisher: American Chemical Society}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/6GSEGUQJ/Enami et al. - 2007 - Global Inorganic Source of Atmospheric Bromine.pdf:application/pdf}, +} + +@article{sakamoto_direct_2009, + title = {Direct Emission of I2 Molecule and {IO} Radical from the Heterogeneous Reactions of Gaseous Ozone with Aqueous Potassium Iodide Solution}, + volume = {113}, + issn = {1089-5639}, + url = {https://doi.org/10.1021/jp903486u}, + doi = {10.1021/jp903486u}, + abstract = {Recent studies indicated that gaseous halogens mediate key tropospheric chemical processes. The inclusion of halogen-ozone chemistry in atmospheric box models actually closes the ∼50\% gap between estimated and measured ozone losses in the marine boundary layer. The additional source of gaseous halogens is deemed to involve previously unaccounted for reactions of O3(g) with sea surface water and marine aerosols. Here, we report that molecular iodine, I2(g), and iodine monoxide radical, {IO}(g), are released ([I2(g)] {\textgreater} 100[{IO}(g)]) during the heterogeneous reaction of gaseous ozone, O3(g), with aqueous potassium iodide, {KI}(aq). It was found that (1) the amounts of I2(g) and {IO}(g) produced are directly proportional to [{KI}(aq)] up to 5 {mM} and (2) {IO}(g) yields are independent of bulk {pH} between 2 and 11, whereas I2(g) production is markedly enhanced at {pH} {\textless} 4. We propose that O3(g) reacts with I− at the air/water interface to produce I2(g) and {IO}(g) via {HOI} and {IOOO}− intermediates, respectively.}, + pages = {7707--7713}, + number = {27}, + journaltitle = {The Journal of Physical Chemistry A}, + shortjournal = {J. Phys. Chem. A}, + author = {Sakamoto, Yosuke and Yabushita, Akihiro and Kawasaki, Masahiro and Enami, Shinichi}, + urldate = {2025-04-29}, + date = {2009-07-09}, + note = {Publisher: American Chemical Society}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/PGFDCQYJ/Sakamoto et al. - 2009 - Direct Emission of I2 Molecule and IO Radical from the Heterogeneous Reactions of Gaseous Ozone with.pdf:application/pdf}, +} + +@article{muramatsu_recycling_2001, + title = {Recycling of iodine in fore-arc areas: evidence from the iodine brines in Chiba, Japan}, + volume = {192}, + issn = {0012-821X}, + url = {https://www.sciencedirect.com/science/article/pii/S0012821X01004836}, + doi = {10.1016/S0012-821X(01)00483-6}, + shorttitle = {Recycling of iodine in fore-arc areas}, + abstract = {The distribution of iodine in the Earth’s crust is dominated by its accumulation in marine sediments. If fluxes between terrestrial and marine compartments are considered, however, a significant imbalance exists between known sources and sinks of iodine. We present here evidence from the fore-arc area near Chiba, Japan, the world’s largest brine-iodine producing area, that iodine is mobilized from marine sediments during the early stages of subduction. Based on detailed chemical analyses of 22 brines and 129I dating of 13 of these samples collected from the Kazusa Formation, we show that iodine in these fluids is derived from organic-rich marine sediments with a minimum age of 50 Myr. Geochemical characteristics of the brines and the age of the iodine indicate that the iodine enrichment is caused by mobilization from subducting marine sediments and not by derivation from the host formation (age 1–2 Myr). The direct return of iodine from marine sediments into the oceans during the subduction of oceanic plates could provide the missing link in the iodine cycle and be an important pathway also in the marine cycle of carbon.}, + pages = {583--593}, + number = {4}, + journaltitle = {Earth and Planetary Science Letters}, + shortjournal = {Earth and Planetary Science Letters}, + author = {Muramatsu, Yasuyuki and Fehn, Udo and Yoshida, Satoshi}, + urldate = {2025-05-01}, + date = {2001-11-15}, + keywords = {iodine, absolute age, brines, fore-arc basins, methane, recycling}, + file = {PDF:/Users/davidtschan/Zotero/storage/35LP25QT/Muramatsu et al. - 2001 - Recycling of iodine in fore-arc areas evidence from the iodine brines in Chiba, Japan.pdf:application/pdf;ScienceDirect Snapshot:/Users/davidtschan/Zotero/storage/7LFI7W4D/S0012821X01004836.html:text/html}, +} + +@article{ammann_multiphase_2024, + title = {Multiphase Chemistry in the Atmosphere}, + volume = {78}, + rights = {https://creativecommons.org/licenses/by/4.0}, + issn = {2673-2424, 0009-4293}, + url = {https://www.chimia.ch/chimia/article/view/2024_754}, + doi = {10.2533/chimia.2024.754}, + abstract = {Earth’s atmosphere comprises a complex mix of gas and condensed phases, where condensed phases facilitate multiphase chemical reactions that would not occur in the gas phase alone. These reactions drive dynamic physical and chemical processes across various spatial and temporal scales, playing a crucial role in the cycling of atmospheric trace constituents. Multiphase chemistry significantly influences geochemical cycles, human health, and climate. This review focuses on the chemical steps governing the cycling of important species, such as halogens, reactive nitrogen, and organics, within aerosol particles, a key type of atmospheric condensed phases, and at condensed phase–air interfaces. These interfaces include mineral oxides, ice, and aqueous solutions found in particulate matter, clouds, snow, and on oceanic and terrestrial surfaces. This review also discusses the important role of redox chemical cycling, the hydrogen bonding network and water activity in these processes.}, + pages = {754--761}, + number = {11}, + journaltitle = {{CHIMIA}}, + shortjournal = {Chimia}, + author = {Ammann, Markus and Alpert, Peter A. and Artiglia, Luca and Bao, Fengxia and Bartels-Rausch, Thorsten and Flórez Ospina, Juan Felipe and Garner, Natasha M. and Iezzi, Lucia and Kilchhofer, Kevin and Laso, Andrés and Longetti, Luca and Mahrt, Fabian}, + urldate = {2025-06-24}, + date = {2024-11-27}, + langid = {english}, + keywords = {Unread}, + file = {PDF:/Users/davidtschan/Zotero/storage/LKG6CSI7/Ammann et al. - 2024 - Multiphase Chemistry in the Atmosphere.pdf:application/pdf}, +} + +@article{chen_impact_2021, + title = {Impact of Tetrabutylammonium on the Oxidation of Bromide by Ozone}, + volume = {5}, + rights = {https://creativecommons.org/licenses/by-nc-nd/4.0/}, + issn = {2472-3452, 2472-3452}, + url = {https://pubs.acs.org/doi/10.1021/acsearthspacechem.1c00233}, + doi = {10.1021/acsearthspacechem.1c00233}, + abstract = {The reaction of ozone with sea-salt derived bromide is relevant for marine boundary layer atmospheric chemistry. The oxidation of bromide by ozone is enhanced at aqueous interfaces. Ocean surface water and sea spray aerosol are enriched in organic compounds, which may also have a significant effect on this reaction at the interface. Here, we assess the surface propensity of cationic tetrabutylammonium at the aqueous liquid−vapor interface by liquid microjet X-ray photoelectron spectroscopy ({XPS}) and the effect of this surfactant on ozone uptake to aqueous bromide solutions. The results clearly indicate that the positively charged nitrogen group in tetrabutylammonium ({TBA}), along with its surface activity, leads to an enhanced interfacial concentration of both bromide and the bromide ozonide reaction intermediate. In parallel, off-line kinetic experiments for the same system demonstrate a strongly enhanced ozone loss rate in the presence of {TBA}, which is attributed to an enhanced surface reaction rate. We used liquid jet {XPS} to obtain detailed chemical composition information from the aqueous-solution−vapor interface of mixed aqueous solutions containing bromide or bromide and chloride with and without {TBA} surfactant. Core level spectra of Br 3d, C 1s, Cl 2p, N 1s, and O 1s were used for this comparison. A model was developed to account for the attenuation of photoelectrons by the carbon-rich layer established by the {TBA} surfactant. We observed that the interfacial density of bromide is increased by an order of magnitude in solutions with {TBA}. The salting-out of {TBA} in the presence of 0.55 M sodium chloride is apparent. The increased interfacial bromide density can be rationalized by the association constants for bromide and chloride to form ion-pairs with {TBA}. Still, the interfacial reactivity is not increasing simply proportionally with the increasing interfacial bromide concentration in response to the presence of {TBA}. The steady state concentration of the bromide ozonide intermediate increases by a smaller degree, and the lifetime of the intermediate is 1 order of magnitude longer in the presence of {TBA}. Thus, the influence of cationic surfactants on the reactivity of bromide depends on the details of the complex environment at the interface.}, + pages = {3008--3021}, + number = {11}, + journaltitle = {{ACS} Earth and Space Chemistry}, + shortjournal = {{ACS} Earth Space Chem.}, + author = {Chen, Shuzhen and Artiglia, Luca and Orlando, Fabrizio and Edebeli, Jacinta and Kong, Xiangrui and Yang, Huanyu and Boucly, Anthony and Corral Arroyo, Pablo and Prisle, Nønne and Ammann, Markus}, + urldate = {2025-06-24}, + date = {2021-11-18}, + langid = {english}, + keywords = {Unread}, + file = {PDF:/Users/davidtschan/Zotero/storage/GWULSF52/Chen et al. - 2021 - Impact of Tetrabutylammonium on the Oxidation of Bromide by Ozone.pdf:application/pdf}, +} + +@article{corral_arroyo_halogen_2019, + title = {Halogen activation and radical cycling initiated by imidazole-2-carboxaldehyde photochemistry}, + volume = {19}, + rights = {https://creativecommons.org/licenses/by/4.0/}, + issn = {1680-7324}, + url = {https://acp.copernicus.org/articles/19/10817/2019/}, + doi = {10.5194/acp-19-10817-2019}, + abstract = {Abstract. Atmospheric aerosol particles can contain light-absorbing +organic compounds, also referred to as brown carbon ({BrC}). The ocean surface +and sea spray aerosol particles can also contain light-absorbing organic species +referred to as chromophoric dissolved organic matter ({CDOM}). Many {BrC} and +{CDOM} species can contain carbonyls, dicarbonyls or aromatic carbonyls such +as imidazole-2-carboxaldehyde ({IC}), which may act as photosensitizers +because they form triplet excited states upon {UV}–{VIS} light absorption. These +triplet excited states are strong oxidants and may initiate catalytic +radical reaction cycles within and at the surface of atmospheric aerosol +particles, thereby increasing the production of condensed-phase reactive +oxygen species ({ROS}). Triplet states or {ROS} can also react with halides, +generating halogen radicals and molecular halogen compounds. In particular, +molecular halogens can be released into the gas phase, which is one +halogen activation pathway. In this work, we studied the influence of bromide and +iodide on the photosensitized production and release of hydroperoxy radicals ({HO}2) upon {UV} irradiation of films in a coated wall flow tube ({CWFT}) containing {IC} in a matrix of citric acid ({CA}) irradiated with {UV} light. In addition, we measured the iodine release upon irradiation of {IC} ∕ {CA} films in the {CWFT}. We developed a kinetic model coupling photosensitized {CA} oxidation with condensed-phase halogen chemistry to support data analysis and assessment of atmospheric implications in terms of {HO}2 production and halogen release in sea spray particles. As indicated by the experimental results and confirmed by the model, significant recycling of halogen species occurred via scavenging reactions with {HO}2. These prevented the full and immediate release of the molecular halogen (bromine and iodine) produced. Recycling was stronger at low relative humidity, attributed to diffusion limitations. Our findings also show that the {HO}2 production from {BrC} or {CDOM} photosensitized reactions can increase due to the presence of halides, leading to high {HO}2 turnover, in spite of low release due to the scavenging reactions. We estimated the iodine production within sea salt aerosol particles due to iodide oxidation by ozone (O3) at 5.0×10-6 M s−1 assuming O3 was in Henry's law equilibrium with the particle. However, using an O3 diffusion coefficient of 1×10-12 cm2 s−1, iodine activation in an aged, organic-rich sea spray is estimated to be 5.5×10-8 M s−1. The estimated iodine production from {BrC} photochemistry based on the results reported here amounts to 4.1×10-7 M s−1 and indicates that {BrC} photochemistry can exceed O3 reactive uptake in controlling the rates of iodine activation from sea spray particles under dry or cold conditions +where diffusion is slow within particles.}, + pages = {10817--10828}, + number = {16}, + journaltitle = {Atmospheric Chemistry and Physics}, + shortjournal = {Atmos. Chem. Phys.}, + author = {Corral Arroyo, Pablo and Aellig, Raffael and Alpert, Peter A. and Volkamer, Rainer and Ammann, Markus}, + urldate = {2025-06-24}, + date = {2019-08-27}, + langid = {english}, + keywords = {Unread}, + file = {PDF:/Users/davidtschan/Zotero/storage/95T43NB2/Corral Arroyo et al. - 2019 - Halogen activation and radical cycling initiated by imidazole-2-carboxaldehyde photochemistry.pdf:application/pdf}, +} + +@article{reza_iodine_2024, + title = {Iodine Activation from Iodate Reduction in Aqueous Films via Photocatalyzed and Dark Reactions}, + volume = {8}, + rights = {https://creativecommons.org/licenses/by/4.0/}, + issn = {2472-3452, 2472-3452}, + url = {https://pubs.acs.org/doi/10.1021/acsearthspacechem.4c00224}, + doi = {10.1021/acsearthspacechem.4c00224}, + abstract = {Iodine in the atmosphere destroys ozone and can nucleate particles by formation of iodic acid, {HIO}3. Recent field observations suggest iodate recycles from particles sustaining significant gas-phase {IO} radical concentrations (0.06 pptv) in aged stratospheric air, and in elevated dust plumes. However, laboratory evidence for iodine activation from aerosols is currently missing. Here, a series of coated-wall flow tube ({CWFT}) experiments test for iodine release from thin aqueous films containing iodate. Photocatalyzed reactions were studied using iron({III}) citrate (Fe−Cit), Arizona Test Dust ({ATD}), and Fe2O3, along with the dark reaction of iodate with H2O2 at 90\% {RH} and 293 K. Fresh films were separately irradiated with visible and {UV}-A light, and the efficient release of molecular iodine, I2, was observed from all irradiated films containing photocatalysts. For films with Fe−Cit, visible light reduced larger amounts of iodate than {UV}-A light, activating ∼40\% of iodate as I2. The formation of oxygenated volatile organic compounds ({OVOC}) and iodinated {OVOC} was also observed. Dark exposure of films to H2O2 led to I2 release in smaller amounts than suggested by Bray−Liebhafsky kinetics, consistent with H2O2 salting-out in the films, or possibly other reasons. Photochemical activation is enhanced by dust proxies in the film, and by aging the film with H2O2 in the dark prior to irradiation. These findings help explain recent field observations of elevated {IO} radical concentrations in lofted dust layers, and warrant the inclusion of photocatalyzed iodate reduction in atmospheric models.}, + pages = {2495--2508}, + number = {12}, + journaltitle = {{ACS} Earth and Space Chemistry}, + shortjournal = {{ACS} Earth Space Chem.}, + author = {Reza, Mago and Iezzi, Lucia and Finkenzeller, Henning and Roose, Antoine and Ammann, Markus and Volkamer, Rainer}, + urldate = {2025-06-24}, + date = {2024-12-19}, + langid = {english}, + keywords = {Aerosol, Read}, + file = {PDF:/Users/davidtschan/Zotero/storage/UPX6W94Q/Reza et al. - 2024 - Iodine Activation from Iodate Reduction in Aqueous Films via Photocatalyzed and Dark Reactions.pdf:application/pdf;sp4c00224_si_001:/Users/davidtschan/Zotero/storage/84D5IXQB/sp4c00224_si_001.pdf:application/pdf}, +} + +@article{wu_emission_2025, + title = {Emission of marine microbes via sea spray aerosol generation: Enrichment, influencing factors and the potential role in marine carbon cycle}, + volume = {359}, + issn = {13522310}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S135223102500336X}, + doi = {10.1016/j.atmosenv.2025.121361}, + shorttitle = {Emission of marine microbes via sea spray aerosol generation}, + pages = {121361}, + journaltitle = {Atmospheric Environment}, + shortjournal = {Atmospheric Environment}, + author = {Wu, Linyao and Liu, Ting and Zhang, Yingyi and Shen, Yuhan and Yao, Yinxi and Ruan, Zhaokang and Tham, Yee Jun and Song, Wei and Huang, Shan and Li, Jun and Lai, Senchao}, + urldate = {2025-08-12}, + date = {2025-10}, + langid = {english}, + keywords = {Microbes, Algae, Microbial Enrichment, Unread}, + file = {PDF:/Users/davidtschan/Zotero/storage/SRMIQL96/Wu et al. - 2025 - Emission of marine microbes via sea spray aerosol generation Enrichment, influencing factors and th.pdf:application/pdf}, +} + +@article{li_technical_2018, + title = {Technical note: Influence of surface roughness and local turbulence on coated-wall flow tube experiments for gas uptake and kinetic studies}, + volume = {18}, + rights = {https://creativecommons.org/licenses/by/3.0/}, + issn = {1680-7324}, + url = {https://acp.copernicus.org/articles/18/2669/2018/}, + doi = {10.5194/acp-18-2669-2018}, + shorttitle = {Technical note}, + abstract = {Abstract. Coated-wall flow tube reactors are frequently used to investigate gas uptake and heterogeneous or multiphase reaction kinetics under laminar flow conditions. Coating surface roughness may potentially distort the laminar flow pattern, induce turbulence and introduce uncertainties in the calculated uptake coefficient based on molecular diffusion assumptions (e.g., Brown/Cooney–Kim–Davis ({CKD})/Knopf–Pöschl–Shiraiwa ({KPS}) methods), which has not been fully resolved in earlier studies. Here, we investigate the influence of surface roughness and local turbulence on coated-wall flow tube experiments for gas uptake and kinetic studies. According to laminar boundary theory and considering the specific flow conditions in a coated-wall flow tube, we derive and propose a critical height δc to evaluate turbulence effects in the design and analysis of coated-wall flow tube experiments. If a geometric coating thickness δg is larger than δc, the roughness elements of the coating may cause local turbulence and result in overestimation of the real uptake coefficient (γ). We further develop modified {CKD}/{KPS} methods (i.e., {CKD}-{LT}/{KPS}-{LT}) to account for roughness-induced local turbulence effects. By combination of the original methods and their modified versions, the maximum error range of γ{CKD} (derived with the {CKD} method) or γ{KPS} (derived with the {KPS} method) can be quantified and finally γ can be constrained. When turbulence is generated, γ{CKD} or γ{KPS} can bear large difference compared to γ. Their difference becomes smaller for gas reactants with lower uptake (i.e., smaller γ) and/or for a smaller ratio of the geometric coating thickness to the flow tube radius (δg ∕ R0). On the other hand, the critical height δc can also be adjusted by optimizing flow tube configurations and operating conditions (i.e., tube diameter, length, and flow velocity), to ensure not only unaffected laminar flow patterns but also other specific requirements for an individual flow tube experiment. We use coating thickness values from previous coated-wall flow tube studies to assess potential roughness effects using the δc criterion. In most studies, the coating thickness was sufficiently small to avoid complications, but some may have been influenced by surface roughness and local turbulence effects.}, + pages = {2669--2686}, + number = {4}, + journaltitle = {Atmospheric Chemistry and Physics}, + shortjournal = {Atmos. Chem. Phys.}, + author = {Li, Guo and Su, Hang and Kuhn, Uwe and Meusel, Hannah and Ammann, Markus and Shao, Min and Pöschl, Ulrich and Cheng, Yafang}, + urldate = {2025-08-12}, + date = {2018-02-23}, + langid = {english}, + keywords = {Coated-Wall Flow Tube, {CWFT}, Unread}, + file = {PDF:/Users/davidtschan/Zotero/storage/Y3EI7BVU/Li et al. - 2018 - Technical note Influence of surface roughness and local turbulence on coated-wall flow tube experim.pdf:application/pdf}, +} + +@thesis{iezzi_interplay_2024, + title = {Interplay between Reactive Oxygen Species, Transition Metals, Nitrogen Oxides and Iodine Species, and its Impact on Multiphase Atmospheric Chemistry}, + url = {http://hdl.handle.net/20.500.11850/718065}, + institution = {{ETH} Zurich}, + type = {phdthesis}, + author = {Iezzi, Lucia}, + editora = {{Ammann, Markus} and {McNeill, Kristopher} and {George, Christian}}, + editoratype = {collaborator}, + urldate = {2025-09-10}, + date = {2024}, + langid = {english}, + doi = {10.3929/ETHZ-B-000718065}, + note = {Artwork Size: 240 p. +Medium: application/pdf +Pages: 240 p.}, + keywords = {Chemistry, info:eu-repo/classification/ddc/540, Unread}, + file = {PDF:/Users/davidtschan/Zotero/storage/6BS5CVXG/Iezzi - 2024 - Interplay between Reactive Oxygen Species, Transition Metals, Nitrogen Oxides and Iodine Species, an.pdf:application/pdf}, +} + +@article{schmitz_kinetics_2012, + title = {Kinetics of the iodate reduction by hydrogen peroxide and relation with the Briggs–Rauscher and Bray–Liebhafsky oscillating reactions}, + volume = {14}, + issn = {1463-9084}, + url = {https://pubs.rsc.org/en/content/articlelanding/2012/cp/c2cp23805e}, + doi = {10.1039/C2CP23805E}, + abstract = {The iodate reduction by hydrogen peroxide in acidic solutions is part of the Bray–Liebhafsky and Briggs–Rauscher oscillating reactions. At low hydrogen peroxide concentrations, typical of the Bray–Liebhafsky reaction, its rate law is with , 7.8 × 10−7 (39°), 1.4 × 10−5 M−1 s−1 (60°) and , 6.2 × 10−5 (39°), 6.3 × 10−4 M−2 s−1 (60°). It is explained by a non-radical mechanism. At high hydrogen peroxide concentrations, typical of the Briggs–Rauscher reaction, a new reaction pathway appears with a rate more than proportional to [H2O2]2 and nearly independent of [{IO}3−] {\textgreater} 0.01 M. This pathway is inhibited by scavengers of free radicals. We suggest that it has a radical mechanism starting with {IOH} + H2O2 ⇌ {IOOH} + H2O and {IOOH}+H2O2 → {IO}˙ + H2O+{HOO}˙.}, + pages = {5711--5717}, + number = {16}, + journaltitle = {Physical Chemistry Chemical Physics}, + shortjournal = {Phys. Chem. Chem. Phys.}, + author = {Schmitz, Guy and Furrow, Stanley}, + urldate = {2025-10-09}, + date = {2012-03-28}, + langid = {english}, + note = {Publisher: The Royal Society of Chemistry}, + keywords = {Reading}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/IJF5TZ3F/Schmitz and Furrow - 2012 - Kinetics of the iodate reduction by hydrogen peroxide and relation with the Briggs–Rauscher and Bray.pdf:application/pdf;Supplementary Information PDF:/Users/davidtschan/Zotero/storage/LA2SI8NQ/Schmitz and Furrow - 2012 - Kinetics of the iodate reduction by hydrogen peroxide and relation with the Briggs–Rauscher and Bray.pdf:application/pdf}, +} + +@article{bray_periodic_1921, + title = {A periodic reaction in homogeneous solution and its relation to catalysis}, + volume = {43}, + issn = {0002-7863}, + url = {https://doi.org/10.1021/ja01439a007}, + doi = {10.1021/ja01439a007}, + pages = {1262--1267}, + number = {6}, + journaltitle = {Journal of the American Chemical Society}, + shortjournal = {J. Am. Chem. Soc.}, + author = {Bray, William C.}, + urldate = {2025-10-10}, + date = {1921-06-01}, + note = {Publisher: American Chemical Society}, + keywords = {Reading}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/BAC92EQH/Bray - 1921 - A PERIODIC REACTION IN HOMOGENEOUS SOLUTION AND ITS RELATION TO CATALYSIS..pdf:application/pdf}, +} + +@article{bray_reactions_1931, + title = {Reactions involving hydrogen peroxide, iodine and iodate ion}, + volume = {53}, + issn = {0002-7863}, + url = {https://doi.org/10.1021/ja01352a006}, + doi = {10.1021/ja01352a006}, + pages = {38--44}, + number = {1}, + journaltitle = {Journal of the American Chemical Society}, + shortjournal = {J. Am. Chem. Soc.}, + author = {Bray, William C. and Liebhafsky, Herman A.}, + urldate = {2025-10-10}, + date = {1931-01-01}, + note = {Publisher: American Chemical Society}, + keywords = {Read}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/X3U4NDQN/Bray and Liebhafsky - 1931 - REACTIONS INVOLVING HYDROGEN PEROXIDE, IODINE AND IODATE ION. I. INTRODUCTION.pdf:application/pdf}, +} + +@article{briggs_oscillating_1973, + title = {An oscillating iodine clock}, + volume = {50}, + issn = {0021-9584}, + url = {https://doi.org/10.1021/ed050p496}, + doi = {10.1021/ed050p496}, + abstract = {An oscillating iodine clock reaction that gives striking cyclic changes from colorless to gold to blue using simple reagents.}, + pages = {496}, + number = {7}, + journaltitle = {Journal of Chemical Education}, + shortjournal = {J. Chem. Educ.}, + author = {Briggs, Thomas S. and Rauscher, Warren C.}, + urldate = {2025-10-10}, + date = {1973-07-01}, + note = {Publisher: American Chemical Society}, + keywords = {Unread}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/4TRJQPRT/Briggs and Rauscher - 1973 - An oscillating iodine clock.pdf:application/pdf}, +} + +@article{chang_use_1958, + title = {The Use of Active Iodine as a Water Disinfectant}, + volume = {47}, + rights = {https://www.elsevier.com/tdm/userlicense/1.0/}, + issn = {00959553}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S0095955315346096}, + doi = {10.1002/jps.3030470610}, + pages = {417--423}, + number = {6}, + journaltitle = {Journal of the American Pharmaceutical Association (Scientific ed.)}, + shortjournal = {Journal of the American Pharmaceutical Association (Scientific ed.)}, + author = {Chang, Shih L.}, + urldate = {2025-10-10}, + date = {1958-06}, + langid = {english}, + keywords = {Unread}, + file = {PDF:/Users/davidtschan/Zotero/storage/X7XD7YPU/Chang - 1958 - The Use of Active Iodine as a Water Disinfectant Section of Microbiology, Water Supply and Water.pdf:application/pdf}, +} + +@article{brode_oxydation_1904, + title = {Die Oxydation des Jodions zu Hypojodit als Zwischenstufe einiger Reaktionen}, + volume = {49U}, + rights = {De Gruyter expressly reserves the right to use all content for commercial text and data mining within the meaning of Section 44b of the German Copyright Act.}, + issn = {2196-7156}, + url = {https://www.degruyterbrill.com/document/doi/10.1515/zpch-1904-4916/html}, + doi = {10.1515/zpch-1904-4916}, + abstract = {Article Die Oxydation des Jodions zu Hypojodit als Zwischenstufe einiger Reaktionen was published on July 1, 1904 in the journal Zeitschrift für Physikalische Chemie (volume 49U, issue 1).}, + pages = {208--216}, + number = {1}, + journaltitle = {Zeitschrift für Physikalische Chemie}, + author = {Brode, Johannes}, + urldate = {2025-10-10}, + date = {1904-07-01}, + langid = {german}, + note = {Publisher: De Gruyter (O)}, + keywords = {Unread}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/V4PGTWEX/Brode - 1904 - Die Oxydation des Jodions zu Hypojodit als Zwischenstufe einiger Reaktionen.pdf:application/pdf}, +} + +@article{rice_thermal_1927, + title = {The Thermal Decomposition of Hydrogen Peroxide}, + volume = {31}, + issn = {0092-7325}, + url = {https://doi.org/10.1021/j150279a006}, + doi = {10.1021/j150279a006}, + pages = {1352--1356}, + number = {9}, + journaltitle = {The Journal of Physical Chemistry}, + shortjournal = {J. Phys. Chem.}, + author = {Rice, F. O. and Reiff, O. M.}, + urldate = {2025-10-10}, + date = {1927-09-01}, + note = {Publisher: American Chemical Society}, + keywords = {Unread}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/6ZH7XEHY/Rice and Reiff - 1927 - The Thermal Decomposition of Hydrogen Peroxide.pdf:application/pdf}, +} + +@online{national_center_for_biotechnology_information_pubchem_2025, + title = {{PubChem} Element Summary for {AtomicNumber} 53, Iodine}, + url = {https://pubchem.ncbi.nlm.nih.gov/element/Iodine}, + titleaddon = {{PubChem} Element Summary for {AtomicNumber} 53, Iodine}, + author = {{\textbackslash}\{National Center for Biotechnology Information{\textbackslash}\}}, + urldate = {2025-11-25}, + date = {2025}, + keywords = {Reading}, + file = {Iodine | I (Element) - PubChem:/Users/davidtschan/Zotero/storage/Z35ARFGT/Iodine.html:text/html}, +} + +@incollection{kaiho_physical_2015, + location = {Hoboken}, + title = {Physical Properties of Iodine}, + isbn = {978-1-118-90991-1}, + url = {https://doi.org/10.1002/9781118909911.ch2}, + abstract = {Summary Iodine has a moderate vapor pressure at room temperature and in an open vessel slowly sublimes to a deep violet vapor that is irritating to the eyes, nose, and throat. This chapter tabulates the physical properties of iodine in solid, liquid and gas phases. Iodine dissolves easily in most organic solvents such as hexane, benzene, carbon tetrachloride, and chloroform owing to its lack of polarity, but it is only slightly soluble in water. However, the solubility of elemental iodine in water can be increased by the addition of sodium or potassium iodide. Iodine accepts electrons from the solvent molecule into its lowest unoccupied molecular orbital ({LUMO}). This lowers the energy of the transition from the highest occupied molecular orbital ({HOMO}) of the iodine atom to its {LUMO}, thereby changing the color from the characteristic violet to brown and other colors. The physical properties of the first four halogens are summarized.}, + pages = {7--14}, + booktitle = {Iodine Chemistry and Applications}, + publisher = {John Wiley \& Sons}, + author = {Kaiho, Tatsuo}, + urldate = {2025-11-25}, + date = {2015}, + doi = {10.1002/9781118909911.ch2}, + keywords = {Reading, highest occupied molecular orbital ({HOMO}), iodine atom, lowest unoccupied molecular orbital ({LUMO}), organic solvents, solubility}, + file = {PDF:/Users/davidtschan/Zotero/storage/SYU6XVKN/Kaiho - 2015 - Physical Properties of Iodine.pdf:application/pdf}, +} + +@article{calvert_glossary_1990, + title = {Glossary of atmospheric chemistry terms (Recommendations 1990)}, + volume = {62}, + rights = {De Gruyter expressly reserves the right to use all content for commercial text and data mining within the meaning of Section 44b of the German Copyright Act.}, + issn = {1365-3075}, + url = {https://www.degruyterbrill.com/document/doi/10.1351/pac199062112167/html}, + doi = {10.1351/pac199062112167}, + abstract = {Article Glossary of atmospheric chemistry terms (Recommendations 1990) was published on January 1, 1990 in the journal Pure and Applied Chemistry (volume 62, issue 11).}, + pages = {2167--2219}, + number = {11}, + journaltitle = {Pure and Applied Chemistry}, + author = {Calvert, J. G.}, + urldate = {2025-11-25}, + date = {1990-01-01}, + langid = {english}, + note = {Publisher: De Gruyter}, + keywords = {Reading}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/37CSARY3/Calvert - 1990 - Glossary of atmospheric chemistry terms (Recommendations 1990).pdf:application/pdf}, +} + +@article{slater_atomic_1964, + title = {Atomic Radii in Crystals}, + volume = {41}, + issn = {0021-9606}, + url = {https://doi.org/10.1063/1.1725697}, + doi = {10.1063/1.1725697}, + abstract = {A set of empirical atomic radii has been set up, such that the sum of the radii of two atoms forming a bond in a crystal or molecule gives an approximate value of the internuclear distance. These radii give fair agreement with experiment in over 1200 cases of bonds in all types of crystals and molecules, with an average deviation of about 0.12 Å. The radii are similar to a set suggested by W. L. Bragg in 1920, but refined by consideration of many more crystals. They hold for covalent, metallic, and ionic binding equally well. These radii agree remarkably well with calculated radii of maximum radial charge density in the outermost shells of the atoms, as taken from previously unpublished calculations of D. Liberman, J. T. Waber, and D. T. Cromer, of the Los Alamos Laboratory, by relativistic self‐consistent field calculation, using the exchange correction suggested in 1951 by the present author. There is discussion of the probable reason for this agreement, and discussion of the relation of these radii to the ionic radii of Pauling, Zachariasen, and others, and the tetrahedral and metallic radii of Pauling.}, + pages = {3199--3204}, + number = {10}, + journaltitle = {The Journal of Chemical Physics}, + shortjournal = {J. Chem. Phys.}, + author = {Slater, J. C.}, + urldate = {2025-11-25}, + date = {1964-11-15}, + keywords = {Reading}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/FDAT58MG/Slater - 1964 - Atomic Radii in Crystals.pdf:application/pdf;Snapshot:/Users/davidtschan/Zotero/storage/59QR2J7M/1.html:text/html}, +} + +@article{sun_role_2025, + title = {Role of atomic chlorine in atmospheric volatile organic compound oxidation and secondary organic aerosol formation: a review}, + url = {https://pubs.rsc.org/en/content/articlelanding/2025/ea/d5ea00101c}, + doi = {10.1039/D5EA00101C}, + shorttitle = {Role of atomic chlorine in atmospheric volatile organic compound oxidation and secondary organic aerosol formation}, + journaltitle = {Environmental Science: Atmospheres}, + author = {Sun, Yinghong and Xu, Li and Li, Jianlong and Li, Kun and Tchinda, Narcisse Tsona and Du, Lin}, + urldate = {2025-11-26}, + date = {2025}, + langid = {english}, + note = {Publisher: Royal Society of Chemistry}, + keywords = {Unread}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/UK37VYGZ/Sun et al. - 2025 - Role of atomic chlorine in atmospheric volatile organic compound oxidation and secondary organic aer.pdf:application/pdf}, +} + +@article{atkinson_evaluated_2007, + title = {Evaluated kinetic and photochemical data for atmospheric chemistry: Volume {III} – gas phase reactions of inorganic halogens}, + volume = {7}, + issn = {1680-7316}, + url = {https://acp.copernicus.org/articles/7/981/2007/}, + doi = {10.5194/acp-7-981-2007}, + shorttitle = {Evaluated kinetic and photochemical data for atmospheric chemistry}, + abstract = {This article, the third in the series, presents kinetic and photochemical data evaluated by the {IUPAC} Subcommittee on Gas Kinetic Data Evaluation for Atmospheric Chemistry. It covers the gas phase and photochemical reactions of inorganic halogen species, which were last published in J. Phys. Chem. Ref. Data, in 2000 (Atkinson et al., 2000), were updated on the {IUPAC} website in 2003 and are updated again in the present evaluation. The article consists of a summary sheet, containing the recommended kinetic parameters for the evaluated reactions, and five appendices containing the data sheets, which provide information upon which the recommendations were made.}, + pages = {981--1191}, + number = {4}, + journaltitle = {Atmospheric Chemistry and Physics}, + author = {Atkinson, R. and Baulch, D. L. and Cox, R. A. and Crowley, J. N. and Hampson, R. F. and Hynes, R. G. and Jenkin, M. E. and Rossi, M. J. and Troe, J.}, + urldate = {2025-11-26}, + date = {2007-02-22}, + note = {Publisher: Copernicus {GmbH}}, + keywords = {Unread, Reference Book}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/DGXBRRTR/Atkinson et al. - 2007 - Evaluated kinetic and photochemical data for atmospheric chemistry Volume III &ndash\; gas phase rea.pdf:application/pdf}, +} + +@article{koenig_quantitative_2020, + title = {Quantitative detection of iodine in the stratosphere}, + volume = {117}, + url = {https://www.pnas.org/doi/abs/10.1073/pnas.1916828117}, + doi = {10.1073/pnas.1916828117}, + abstract = {Oceanic emissions of iodine destroy ozone, modify oxidative capacity, and can form +new particles in the troposphere. However, the impact of iodine ...}, + pages = {1860--1866}, + number = {4}, + journaltitle = {Proceedings of the National Academy of Sciences}, + author = {Koenig, Theodore K. and Baidar, Sunil and Campuzano-Jost, Pedro and Cuevas, Carlos A. and Dix, Barbara and Fernandez, Rafael P. and Guo, Hongyu and Hall, Samuel R. and Kinnison, Douglas and Nault, Benjamin A. and Ullmann, Kirk and Jimenez, Jose L. and Saiz-Lopez, Alfonso and Volkamer, Rainer}, + urldate = {2025-11-26}, + date = {2020-01-28}, + note = {Company: National Academy of Sciences +Distributor: National Academy of Sciences +Institution: National Academy of Sciences +Label: National Academy of Sciences +Publisher: Proceedings of the National Academy of Sciences}, + keywords = {Unread}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/77HYFX4N/Koenig et al. - 2020 - Quantitative detection of iodine in the stratosphere.pdf:application/pdf;pnas.1916828117.sapp:/Users/davidtschan/Zotero/storage/JJMNBXMH/pnas.1916828117.sapp.pdf:application/pdf}, +} + +@article{cuevas_influence_2022, + title = {The influence of iodine on the Antarctic stratospheric ozone hole}, + volume = {119}, + rights = {Copyright © 2022 the Author(s). Published by {PNAS}.}, + url = {https://www.pnas.org/doi/abs/10.1073/pnas.2110864119}, + doi = {10.1073/pnas.2110864119}, + abstract = {The catalytic depletion of Antarctic stratospheric ozone is linked to anthropogenic +emissions of chlorine and bromine. Despite its larger ozone-dep...}, + pages = {e2110864119}, + number = {7}, + journaltitle = {Proceedings of the National Academy of Sciences}, + author = {Cuevas, Carlos A. and Fernandez, Rafael P. and Kinnison, Douglas E. and Li, Qinyi and Lamarque, Jean-François and Trabelsi, Tarek and Francisco, Joseph S. and Solomon, Susan and Saiz-Lopez, Alfonso}, + urldate = {2025-11-26}, + date = {2022-02-15}, + note = {Company: National Academy of Sciences +Distributor: National Academy of Sciences +Institution: National Academy of Sciences +Label: National Academy of Sciences +Publisher: Proceedings of the National Academy of Sciences}, + keywords = {Unread}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/FNSTJEEU/Cuevas et al. - 2022 - The influence of iodine on the Antarctic stratospheric ozone hole.pdf:application/pdf}, +} + +@article{jziemann_kinetics_2012, + title = {Kinetics, products, and mechanisms of secondary organic aerosol formation}, + volume = {41}, + url = {https://pubs.rsc.org/en/content/articlelanding/2012/cs/c2cs35122f}, + doi = {10.1039/C2CS35122F}, + pages = {6582--6605}, + number = {19}, + journaltitle = {Chemical Society Reviews}, + author = {J. Ziemann, Paul and Atkinson, Roger}, + urldate = {2025-11-26}, + date = {2012}, + langid = {english}, + note = {Publisher: Royal Society of Chemistry}, + keywords = {Unread}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/QGSP7HFB/J. Ziemann and Atkinson - 2012 - Kinetics, products, and mechanisms of secondary organic aerosol formation.pdf:application/pdf}, +} + +@article{bhattarai_levoglucosan_2019, + title = {Levoglucosan as a tracer of biomass burning: Recent progress and perspectives}, + volume = {220}, + issn = {0169-8095}, + url = {https://www.sciencedirect.com/science/article/pii/S0169809518311098}, + doi = {10.1016/j.atmosres.2019.01.004}, + shorttitle = {Levoglucosan as a tracer of biomass burning}, + abstract = {Biomass burning ({BB}) is a major source of air pollution from local to global scale, having variable effects on air quality, human health, and climate system. Therefore, the source identification and characterization of {BB}-derived aerosols and tracer gases in the ambient environment is crucial. This review provides recent updates on the applicability of levoglucosan as a {BB} tracer in different environmental matrices such as aerosols, marine, snow and ice-cores etc. Among several tracer of {BB} emissions, levoglucosan has recently received widespread attention due to its unique origin solely from the pyrolysis of cellulose and hemicellulose, making it as a robust marker for characterization and quantification of {BB} throughout the world. This review first summarizes the established and emerging analytical methods, and their advantages and disadvantages for measurement of levoglucosan. Second, we discuss the formation mechanism, lifetime and its stability in different environmental conditions. In addition, we also try to deliberate on the application of ratios of levoglucosan with different organic components such as mannosan (M) and organic carbon ({OC}) for better identification of emission sources. Spatial distributions of levoglucosan in different locations (e.g., urban, rural, forest, marine, poles and higher altitude) are discussed scrupulously and meticulously on a global scale. We also reviewed the distributions of levoglucosan in snow, ice core and sediments to understand its applicability to construct paleofire records. Finally, we propose some key recommendations for future work in different ambient environmental conditions by utilizing the ratios of levoglucosan with other compounds (not limited only to M and {OC}) and the use of levoglucosan to reconstruct the paleo-historical records of fire-activity.}, + pages = {20--33}, + journaltitle = {Atmospheric Research}, + shortjournal = {Atmospheric Research}, + author = {Bhattarai, Hemraj and Saikawa, Eri and Wan, Xin and Zhu, Hongxia and Ram, Kirpa and Gao, Shaopeng and Kang, Shichang and Zhang, Qianggong and Zhang, Yulan and Wu, Guangming and Wang, Xiaoping and Kawamura, Kimitaka and Fu, Pingqing and Cong, Zhiyuan}, + urldate = {2025-11-26}, + date = {2019-05-15}, + keywords = {Aerosol, Biomass burning, Levoglucosan, Organic tracer}, + file = {PDF:/Users/davidtschan/Zotero/storage/ZULGVRRI/Bhattarai et al. - 2019 - Levoglucosan as a tracer of biomass burning Recent progress and perspectives.pdf:application/pdf;ScienceDirect Snapshot:/Users/davidtschan/Zotero/storage/5WMKCILH/S0169809518311098.html:text/html}, +} + +@article{lgemoets_liquid_2016, + title = {Liquid phase oxidation chemistry in continuous-flow microreactors}, + volume = {45}, + url = {https://pubs.rsc.org/en/content/articlelanding/2016/cs/c5cs00447k}, + doi = {10.1039/C5CS00447K}, + pages = {83--117}, + number = {1}, + journaltitle = {Chemical Society Reviews}, + author = {L. Gemoets, Hannes P. and Su, Yuanhai and Shang, Minjing and Hessel, Volker and Luque, Rafael and Noël, Timothy}, + urldate = {2025-11-26}, + date = {2016}, + langid = {english}, + note = {Publisher: Royal Society of Chemistry}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/EAILQYXQ/L. Gemoets et al. - 2016 - Liquid phase oxidation chemistry in continuous-flow microreactors.pdf:application/pdf}, +} + +@article{peng_radical_2020, + title = {Radical chemistry in oxidation flow reactors for atmospheric chemistry research}, + volume = {49}, + url = {https://pubs.rsc.org/en/content/articlelanding/2020/cs/c9cs00766k}, + doi = {10.1039/C9CS00766K}, + pages = {2570--2616}, + number = {9}, + journaltitle = {Chemical Society Reviews}, + author = {Peng, Zhe and L. Jimenez, Jose}, + urldate = {2025-11-26}, + date = {2020}, + langid = {english}, + note = {Publisher: Royal Society of Chemistry}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/22C46EHB/Peng and L. Jimenez - 2020 - Radical chemistry in oxidation flow reactors for atmospheric chemistry research.pdf:application/pdf}, +} + +@article{li_secondary_2019, + title = {Secondary organic aerosol formation from \ensuremath{\alpha}-pinene, alkanes, and oil-sands-related precursors in a new oxidation flow reactor}, + volume = {19}, + issn = {1680-7316}, + url = {https://acp.copernicus.org/articles/19/9715/2019/}, + doi = {10.5194/acp-19-9715-2019}, + abstract = {Oil-sands ({OS}) operations in Alberta, Canada, are a large source of secondary organic aerosol ({SOA}). However, the {SOA} formation process from {OS}-related precursors remains poorly understood. In this work, a newly developed oxidation flow reactor ({OFR}), the Environment and Climate Change Canada {OFR} ({ECCC}-{OFR}), was characterized and used to study the yields and composition of {SOA} formed from {OH} oxidation of α-pinene, selected alkanes, and the vapors evolved from five {OS}-related samples ({OS} ore, naphtha, tailings pond water, bitumen, and dilbit). The derived {SOA} yields from α-pinene and selected alkanes using the {ECCC}-{OFR} were in good agreement with those of traditional smog chamber experiments but significantly higher than those of other {OFR} studies under similar conditions. The results also suggest that gas-phase reactions leading to fragmentation (i.e., C–C bond cleavage) have a relatively small impact on the {SOA} yields in the {ECCC}-{OFR} at high photochemical ages, in contrast to other previously reported {OFR} results. Translating the impact of fragmentation reactions in the {ECCC}-{OFR} to ambient atmospheric conditions reduces its impact on {SOA} formation even further. These results highlight the importance of careful evaluation of {OFR} data, particularly when using such data to provide empirical factors for the fragmentation process in models. Application of the {ECCC}-{OFR} to {OS}-related precursor mixtures demonstrated that the {SOA} yields from {OS} ore and bitumen vapors (maximum of ∼0.6–0.7) are significantly higher than those from the vapors from solvent use (naphtha), effluent from {OS} processing (tailings pond water), and from the solvent diluted bitumen (dilbit; maximum of ∼0.2–0.3), likely due to the volatility of each precursor mixture. A comparison of the yields and elemental ratios (H∕C and O∕C) of the {SOA} from the {OS}-related precursors to those of linear and cyclic alkane precursors of similar carbon numbers suggests that cyclic alkanes play an important role in the {SOA} formation in the {OS}. The analysis further indicates that the majority of the {SOA} formed downwind of {OS} facilities is derived from open-pit mining operations (i.e., {OS} ore evaporative emissions) rather than from higher-volatility precursors from solvent use during processing and/or tailings management. The current results have implications for improving the regional modeling of {SOA} from {OS} sources, for the potential mitigation of {OS} precursor emissions responsible for observed {SOA} downwind of {OS} operations, and for the understanding of petrochemical- and alkane-derived {SOA} in general.}, + pages = {9715--9731}, + number = {15}, + journaltitle = {Atmospheric Chemistry and Physics}, + author = {Li, Kun and Liggio, John and Lee, Patrick and Han, Chong and Liu, Qifan and Li, Shao-Meng}, + urldate = {2025-12-01}, + date = {2019-08-01}, + note = {Publisher: Copernicus {GmbH}}, + keywords = {{ECCC}-{OCR}, Reading}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/P5M3SGM7/Li et al. - 2019 - Secondary organic aerosol formation from α-pinene, alkanes, and oil-sands-related precursors.pdf:application/pdf;PDF (Supplement):/Users/davidtschan/Zotero/storage/LCW7QREC/Li et al. - 2019 - Secondary organic aerosol formation from α-pinene, alkanes, and oil-sands-related precursors.pdf:application/pdf}, +} + +@article{ma_oxidation_2025, + title = {Oxidation Flow Reactor and Its Application in Secondary Organic Aerosol Formation in Laboratory Studies}, + volume = {2}, + url = {https://doi.org/10.1021/acsestair.5c00047}, + doi = {10.1021/acsestair.5c00047}, + abstract = {Secondary organic aerosol ({SOA}) is a key component of atmospheric particulate matter that affects air quality and climate. Oxidation flow reactors ({OFRs}) have been widely used in recent years to simulate the formation of {SOA} due to their ability to achieve high oxidation levels, thus becoming a promising complement to traditional smog chambers. This review comprehensively overviews existing {OFRs} and compares their structural differences. It also discusses the research progress on the formation of {SOA} in {OFRs} from various biogenic and anthropogenic organic gas precursors in laboratories. We evaluate the limitations and advancements of various {OFRs} by comparing the {SOA} yield and chemical characteristics obtained from different {OFRs}. Overall, {OFR} is crucial for understanding the formation mechanism of {SOA} and quantifying the contribution of different precursors to atmospheric particulate matter formation. Nevertheless, due to the complexity of {SOA} formation mechanisms in the troposphere, further research is still needed in the design of {OFR}, and the atmospheric oxidation mechanism under the composite system, to provide more accurate data for atmospheric models.}, + pages = {1394--1410}, + number = {8}, + journaltitle = {{ACS} {ES}\&T Air}, + shortjournal = {{ACS} {EST} Air}, + author = {Ma, Xueqi and Li, Kun and Zhang, Shan and Yang, Zhaomin and Xu, Li and Tsona Tchinda, Narcisse and Du, Lin}, + urldate = {2025-12-02}, + date = {2025-08-08}, + note = {Publisher: American Chemical Society}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/PGBVLL6G/Ma et al. - 2025 - Oxidation Flow Reactor and Its Application in Secondary Organic Aerosol Formation in Laboratory Stud.pdf:application/pdf}, +} + +@article{bruns_inter-comparison_2015, + title = {Inter-comparison of laboratory smog chamber and flow reactor systems on organic aerosol yield and composition}, + volume = {8}, + issn = {1867-1381}, + url = {https://amt.copernicus.org/articles/8/2315/2015/amt-8-2315-2015.html}, + doi = {10.5194/amt-8-2315-2015}, + abstract = {A variety of tools are used to simulate atmospheric aging, including smog chambers and flow reactors. Traditional, large-scale smog chambers age emissions over the course of hours to days, whereas flow reactors rapidly age emissions using high oxidant concentrations to reach higher degrees of oxygenation than typically attained in smog chamber experiments. The atmospheric relevance of the products generated under such rapid oxidation warrants further study. However, no previously published studies have compared the yields and chemical composition of products generated in flow reactors and smog chambers from the same starting mixture. + + The yields and composition of the organic aerosol formed from the photo-oxidation of α-pinene and of wood-combustion emissions in a smog chamber ({SC}) and two flow reactors: a potential aerosol mass reactor ({PAM}) and a micro-smog chamber ({MSC}), were determined using aerosol mass spectrometry. Reactants were sampled from the {SC} and aged in the {MSC} and the {PAM} using a range of hydroxyl radical ({OH}) concentrations and then photo-chemically aged in the {SC}. + + The chemical composition, as well as the maximum yields and emission factors, of the products in both the α-pinene and wood-combustion systems determined with the {PAM} and the {SC} agreed reasonably well. High {OH} exposures have been shown previously to lower yields by breaking carbon–carbon bonds and forming higher volatility species, which reside largely in the gas phase; however, fragmentation in the {PAM} was not observed. The yields determined using the {PAM} for the α-pinene system were slightly lower than in the {SC}, possibly from increased wall losses of gas phase species due to the higher surface area to volume ratios in the {PAM}, even when offset with better isolation of the sampled flow from the walls. The α-pinene {SOA} results for the {MSC} were not directly comparable, as particles were smaller than the optimal {AMS} transmission range. The higher supersaturation in the flow reactors resulted in more nucleation than in the {SC}. For the wood-combustion system, emission factors measured from the {MSC} were typically lower than those measured from the {SC}. Lower emission factors in the {MSC} may have been due to considerable nucleation mode particles formed in the {MSC} which were not detected by the {AMS} or due to condensational loss of gases to the walls inside or after the {MSC}. More comprehensive coverage of the potential particle size range is needed in future {SOA} measurements to improve our understanding of the differences in yields when comparing the {MSC} to the {SC}. The {PAM} and the {SC} agreed within measurement uncertainties in terms of yields and composition for the systems and conditions studied here and this agreement supports the continued use of the {PAM} to study atmospheric aging.}, + pages = {2315--2332}, + number = {6}, + journaltitle = {Atmospheric Measurement Techniques}, + author = {Bruns, E. A. and El Haddad, I. and Keller, A. and Klein, F. and Kumar, N. K. and Pieber, S. M. and Corbin, J. C. and Slowik, J. G. and Brune, W. H. and Baltensperger, U. and Prévôt, A. S. H.}, + urldate = {2025-12-02}, + date = {2015-06-04}, + note = {Publisher: Copernicus {GmbH}}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/SUN4W4LB/Bruns et al. - 2015 - Inter-comparison of laboratory smog chamber and flow reactor systems on organic aerosol yield and co.pdf:application/pdf}, +} + +@article{han_secondary_2022, + title = {Secondary organic aerosols from {OH} oxidation of cyclic volatile methyl siloxanes as an important Si source in the atmosphere}, + volume = {22}, + issn = {1680-7316}, + url = {https://acp.copernicus.org/articles/22/10827/2022/}, + doi = {10.5194/acp-22-10827-2022}, + abstract = {Cyclic volatile methyl siloxanes ({cVMSs}), which can volatilize into the atmosphere, are active ingredients in widely used consumer products, thus attracting much attention due to their potential environmental risks. While in the atmosphere the {cVMSs} undergo oxidation, yielding both gaseous and particulate products. The aerosol yields and compositions from the {OH} oxidation of four {cVMSs} (D3–D6) were determined under low- and high-{NOx} conditions in an oxidation flow reactor. The aerosol yields increased progressively from D3 to D6, consistent with the volatilities and molecule weights of these {cVMSs}. {NOx} can restrict the formation of secondary organic aerosols ({SOAs}), leading to lower {SOA} yields under high-{NOx} conditions than under low-{NOx} conditions, with a yield decrease between 0.05–0.30 depending on the {cVMSs}. Ammonium sulfate seeds exhibited minor impacts on {SOA} yields under low-{NOx} conditions but significantly increased the {SOA} yields in the oxidation of D3–D5 at short photochemical ages under high-{NOx} conditions. The mass spectra of the {SOAs} showed a dependence of its chemical compositions on {OH} exposure. At high exposures equivalent to photochemical ages of \>4 d in the atmosphere, D4–D6 {SOAs} mainly consisted of {CxHy} and {CxHyOzSin} under low-{NOx} conditions, whereas they primarily contained {NmOz}, {CxHy}, {CxHyO}1, {CxHyO}\>1 and {CxHyOzSin} under high-{NOx} conditions. The potential contributions of {cVMSs} to {SOA} formation in the atmosphere were evaluated using the reported {cVMSs} annual production and the yield obtained in the present study. A global {cVMS}-derived (D4–D6) {SOA} source strength is estimated to be 0.01 Tg yr−1, distributed over major urban centers.}, + pages = {10827--10839}, + number = {16}, + journaltitle = {Atmospheric Chemistry and Physics}, + author = {Han, Chong and Yang, Hongxing and Li, Kun and Lee, Patrick and Liggio, John and Leithead, Amy and Li, Shao-Meng}, + urldate = {2025-12-02}, + date = {2022-08-26}, + note = {Publisher: Copernicus {GmbH}}, + keywords = {Unread, {ECCC}-{OCR}}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/F4XWYJ22/Han et al. - 2022 - Secondary organic aerosols from OH oxidation of cyclic volatile methyl siloxanes as an important Si.pdf:application/pdf;PDF (Supplement):/Users/davidtschan/Zotero/storage/L357Q9GA/Han et al. - 2022 - Secondary organic aerosols from OH oxidation of cyclic volatile methyl siloxanes as an important Si.pdf:application/pdf}, +} + +@article{bianchi_highly_2019, + title = {Highly Oxygenated Organic Molecules ({HOM}) from Gas-Phase Autoxidation Involving Peroxy Radicals: A Key Contributor to Atmospheric Aerosol}, + volume = {119}, + issn = {0009-2665}, + url = {https://doi.org/10.1021/acs.chemrev.8b00395}, + doi = {10.1021/acs.chemrev.8b00395}, + shorttitle = {Highly Oxygenated Organic Molecules ({HOM}) from Gas-Phase Autoxidation Involving Peroxy Radicals}, + abstract = {Highly oxygenated organic molecules ({HOM}) are formed in the atmosphere via autoxidation involving peroxy radicals arising from volatile organic compounds ({VOC}). {HOM} condense on pre-existing particles and can be involved in new particle formation. {HOM} thus contribute to the formation of secondary organic aerosol ({SOA}), a significant and ubiquitous component of atmospheric aerosol known to affect the Earth’s radiation balance. {HOM} were discovered only very recently, but the interest in these compounds has grown rapidly. In this Review, we define {HOM} and describe the currently available techniques for their identification/quantification, followed by a summary of the current knowledge on their formation mechanisms and physicochemical properties. A main aim is to provide a common frame for the currently quite fragmented literature on {HOM} studies. Finally, we highlight the existing gaps in our understanding and suggest directions for future {HOM} research.}, + pages = {3472--3509}, + number = {6}, + journaltitle = {Chemical Reviews}, + shortjournal = {Chem. Rev.}, + author = {Bianchi, Federico and Kurtén, Theo and Riva, Matthieu and Mohr, Claudia and Rissanen, Matti P. and Roldin, Pontus and Berndt, Torsten and Crounse, John D. and Wennberg, Paul O. and Mentel, Thomas F. and Wildt, Jürgen and Junninen, Heikki and Jokinen, Tuija and Kulmala, Markku and Worsnop, Douglas R. and Thornton, Joel A. and Donahue, Neil and Kjaergaard, Henrik G. and Ehn, Mikael}, + urldate = {2025-12-10}, + date = {2019-03-27}, + note = {Publisher: American Chemical Society}, + keywords = {Unread}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/ZSJ4IPIB/Bianchi et al. - 2019 - Highly Oxygenated Organic Molecules (HOM) from Gas-Phase Autoxidation Involving Peroxy Radicals A K.pdf:application/pdf}, +} + +@article{calogirou_gas-phase_1999, + title = {Gas-phase terpene oxidation products: a review}, + volume = {33}, + issn = {1352-2310}, + url = {https://www.sciencedirect.com/science/article/pii/S1352231098002775}, + doi = {10.1016/S1352-2310(98)00277-5}, + shorttitle = {Gas-phase terpene oxidation products}, + abstract = {Terpenes are emitted in large quantities from vegetation into the troposphere, where they react readily with ozone, {OH} and {NO}3 radicals leading to a number of oxidation products. The current knowledge about gas-phase terpene oxidation products is reviewed. Their formation and decomposition pathways, their products and their relevance for the troposphere, and their chemical analysis are discussed. Data on oxidation kinetics, and product yields is presented for 23 terpenes and 65 oxidation products. A total of 84 references are quoted.}, + pages = {1423--1439}, + number = {9}, + journaltitle = {Atmospheric Environment}, + shortjournal = {Atmospheric Environment}, + author = {Calogirou, A. and Larsen, B. R. and Kotzias, D.}, + urldate = {2025-12-10}, + date = {1999-04-01}, + keywords = {Ozone, Unread, Monoterpenes, {NO}, {OH}, Sesquiterpenes, Troposphere}, + file = {PDF:/Users/davidtschan/Zotero/storage/5RJVQMJP/Calogirou et al. - 1999 - Gas-phase terpene oxidation products a review.pdf:application/pdf;ScienceDirect Snapshot:/Users/davidtschan/Zotero/storage/UG6QRWNT/S1352231098002775.html:text/html}, +} + +@article{aliceupshur_organic_2023, + title = {Organic synthesis in the study of terpene-derived oxidation products in the atmosphere}, + volume = {40}, + url = {https://pubs.rsc.org/en/content/articlelanding/2023/np/d2np00064d}, + doi = {10.1039/D2NP00064D}, + pages = {890--921}, + number = {4}, + journaltitle = {Natural Product Reports}, + author = {Alice Upshur, Mary and Gray Bé, Ariana and Luo, Jingyi and G. Varelas, Jonathan and M. Geiger, Franz and J. Thomson, Regan}, + urldate = {2025-12-10}, + date = {2023}, + langid = {english}, + note = {Publisher: Royal Society of Chemistry}, + keywords = {Unread}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/FUND34XE/Alice Upshur et al. - 2023 - Organic synthesis in the study of terpene-derived oxidation products in the atmosphere.pdf:application/pdf}, +} + +@article{claeys_secondary_2021, + title = {Secondary Organic Aerosol Formation from Isoprene: Selected Research, Historic Account and State of the Art}, + volume = {12}, + rights = {http://creativecommons.org/licenses/by/3.0/}, + issn = {2073-4433}, + url = {https://www.mdpi.com/2073-4433/12/6/728}, + doi = {10.3390/atmos12060728}, + shorttitle = {Secondary Organic Aerosol Formation from Isoprene}, + abstract = {In this review, we cover selected research on secondary organic aerosol ({SOA}) formation from isoprene, from the beginning of research, about two decades ago, to today. The review begins with the first observations of isoprene {SOA} markers, i.e., 2-methyltetrols, in ambient fine aerosol and focuses on studies dealing with molecular characterization, speciation, formation mechanisms, and source apportionment. A historic account is given on how research on isoprene {SOA} has developed. The isoprene {SOA} system is rather complex, with different pathways being followed in pristine and polluted conditions. For {SOA} formation from isoprene, acid-catalyzed hydrolysis is necessary, and sulfuric acid enhances {SOA} by forming additional nonvolatile products such as organosulfates. Certain results reported in early papers have been re-interpreted in the light of recent results; for example, the formation of C5-alkene triols. Attention is given to mass spectrometric and separation techniques, which played a crucial role in molecular characterization. The unambiguous structural characterization of isoprene {SOA} markers has been achieved, owing to the preparation of reference compounds. Efforts have also been made to use air quality data to estimate the influence of biogenic and pollution aerosol sources. This review examines the use of an organic marker-based method and positive matrix factorization to apportion {SOA} from different sources, including isoprene {SOA}.}, + pages = {728}, + number = {6}, + journaltitle = {Atmosphere}, + author = {Claeys, Magda and Maenhaut, Willy}, + urldate = {2025-12-10}, + date = {2021-06}, + langid = {english}, + note = {Publisher: Multidisciplinary Digital Publishing Institute}, + keywords = {Unread, 2-methylglyceric acid, 2-methyltetrols, C$_{\textrm{5}}$-alkene triols, {IEPOX}, isoprene, organosulfates, particulate matter, secondary organic aerosol, source apportionment}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/VWYVM9QS/Claeys and Maenhaut - 2021 - Secondary Organic Aerosol Formation from Isoprene Selected Research, Historic Account and State of.pdf:application/pdf}, +} + +@article{srivastava_formation_2022, + title = {Formation of secondary organic aerosols from anthropogenic precursors in laboratory studies}, + volume = {5}, + rights = {2022 The Author(s)}, + issn = {2397-3722}, + url = {https://www.nature.com/articles/s41612-022-00238-6}, + doi = {10.1038/s41612-022-00238-6}, + abstract = {Aerosols produced from the oxidation of volatile/semi-volatile organic compounds ({VOCs}/{SVOCs}), known as secondary organic aerosol ({SOA}), account for a significant fraction of atmospheric airborne particles. This paper reviews the current understanding of {SOA} formation from gas-phase oxidation with a focus on anthropogenic precursors and their reaction products from atmospheric simulation chamber studies. The review summarises the major reaction products derived from main groups of {SOA} precursors (e.g., alkanes, aromatics), {SOA} yields and the factors controlling {SOA} formation. We highlight that lab-derived {SOA} yield depends strongly upon, not only the concentrations of {SOA} precursors and oxidants but also simulation conditions.}, + pages = {22}, + number = {1}, + journaltitle = {npj Climate and Atmospheric Science}, + shortjournal = {npj Clim Atmos Sci}, + author = {Srivastava, Deepchandra and Vu, Tuan V. and Tong, Shengrui and Shi, Zongbo and Harrison, Roy M.}, + urldate = {2025-12-10}, + date = {2022-03-24}, + langid = {english}, + note = {Publisher: Nature Publishing Group}, + keywords = {Atmospheric chemistry}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/ZM28CZFW/Srivastava et al. - 2022 - Formation of secondary organic aerosols from anthropogenic precursors in laboratory studies.pdf:application/pdf}, +} + +@article{snyder_origin_2002, + title = {Origin of iodine in volcanic fluids: 129I results from the Central American Volcanic Arc}, + volume = {66}, + issn = {0016-7037}, + url = {https://www.sciencedirect.com/science/article/pii/S0016703702008256}, + doi = {10.1016/S0016-7037(02)00825-6}, + shorttitle = {Origin of iodine in volcanic fluids}, + abstract = {The largest reservoir of crustal iodine is found in marine sediments, where it is closely associated with organic material. This presence, together with the existence of a long-lived, cosmogenic radioisotope 129I (t1/2 = 15.7 Ma), make this isotopic system well suited for the study of sediment recycling in subduction zones. Reported here are the results of 129I/I ratios in volcanic fluids, collected during a comprehensive study of fluids and gases in the Central American Volcanic Arc. 129I/I ratios, together with I, Br, and Cl concentrations, were determined in 79 samples from four geothermal centers and a number of crater lakes, fumaroles, hot springs, and surface waters in Costa Rica, Nicaragua, and El Salvador. Geothermal and volcanic fluids were found to have iodine concentrations substantially higher than values in seawater or meteoric waters. 129I/I ratios in most of the geothermal fluids are below the preanthropogenic input ratio of 1500 × 10−15, demonstrating that recent anthropogenic additions are largely absent from the volcanic systems. The majority of the 129I/I ratios are between 500 and 800 × 10−15. These ratios indicate minimum iodine ages between 25 and 15 Ma, in good agreement with the age of subducted sediments in this region. In all four geothermal systems, however, a few samples were found with iodine ages older than 40 Ma—that is, considerably below the expected age range for subducted sediments from the Cocos Plate. These samples probably reflect the presence of iodine derived from sediments in older accreted oceanic terraines. The iodine ages indicate that the magmatic end member for the volcanic fluids originates in the deeper parts of the subducted sediment column, with small additions from older iodine mobilized from the overlying crust. The high concentrations of iodine in geothermal fluids, combined with the observed iodine ages, demonstrate that remobilization in the main volcanic zone (and probably also in the forearc area) is an important part in the overall marine cycle of iodine and similar elements.}, + pages = {3827--3838}, + number = {21}, + journaltitle = {Geochimica et Cosmochimica Acta}, + shortjournal = {Geochimica et Cosmochimica Acta}, + author = {Snyder, Glen T and Fehn, Udo}, + urldate = {2025-12-11}, + date = {2002-11-01}, + file = {PDF:/Users/davidtschan/Zotero/storage/5HZAFLEQ/Snyder and Fehn - 2002 - Origin of iodine in volcanic fluids 129I results from the Central American Volcanic Arc.pdf:application/pdf;ScienceDirect Snapshot:/Users/davidtschan/Zotero/storage/354DE3SQ/S0016703702008256.html:text/html}, +} + +@article{kennedy_iodine_1987, + title = {Iodine diagenesis in pelagic deep-sea sediments}, + volume = {51}, + issn = {0016-7037}, + url = {https://www.sciencedirect.com/science/article/pii/0016703787903000}, + doi = {10.1016/0016-7037(87)90300-0}, + abstract = {Nineteen sediment cores from the Madeira, Seine, Tagus and Nares Abyssal Plains and the Alboran Sea have been used to evaluate the speciation, fluxes and diagenesis of iodine in the deep sea. The sediments have surficial molar I/C ratios of 10–30 × 10−4 in excess of previous reported values for planktonic material ({\textasciitilde}1 × 10−4). Solid phase I contents decrease exponentially with depth corresponding to decomposition rate constants of 5–260 × 10−6 yr−1 which vary with the carbon accumulation rate. Iodine species in the pore waters follow a vertical sequence of four zones: 1. a zone of I− production where total dissolved iodine (∑I) concentrations initially increase at the seawater-sediment interface; 2. a zone of I− oxidation where interconversion of I− to {IO}−3 occurs; 3. a zone of {IO}−3 reduction where interconversion of {IO}−3 back to I− occurs which corresponds to the suboxic part of the sediment column; and 4. a further zone of I− production which is confined to the lower anoxic part of the sediment column. Benthic ∑I fluxes in the Madeira Abyssal Plain measured from shipboard incubation experiments and calculated from porewater gradients are similar, averaging 0.55 and 0.36 × 10−8 μmol cm−2 sec−, respectively. In the surface sediment the observed I enrichment results from a quasi-closed cycle for iodine initially involving release of I− from decomposing marine organic matter followed by rapid removal onto organic matter at the sediment-seawater interface where I/C regeneration ratios of up to 200 × 10−4 are found, lodate reduction occurs during suboxic diagenesis, after denitrification and before {MnO}2 reduction, consistent with the sequence of reactions predicted from the free energy yields for organic matter oxidation. There is some further I− production in the anoxic section of sediments but at much smaller rates than occur during the interfacial diagenetic cycling.}, + pages = {2489--2504}, + number = {9}, + journaltitle = {Geochimica et Cosmochimica Acta}, + shortjournal = {Geochimica et Cosmochimica Acta}, + author = {Kennedy, H. A and Elderfield, H}, + urldate = {2025-12-12}, + date = {1987-09-01}, + file = {PDF:/Users/davidtschan/Zotero/storage/68QK8VMQ/Kennedy and Elderfield - 1987 - Iodine diagenesis in pelagic deep-sea sediments.pdf:application/pdf}, +} + +@article{chance_distribution_2014, + title = {The distribution of iodide at the sea surface}, + volume = {16}, + url = {https://pubs.rsc.org/en/content/articlelanding/2014/em/c4em00139g}, + doi = {10.1039/C4EM00139G}, + pages = {1841--1859}, + number = {8}, + journaltitle = {Environmental Science: Processes \& Impacts}, + author = {Chance, Rosie and R. Baker, Alex and Carpenter, Lucy and D. Jickells, Tim}, + urldate = {2025-12-12}, + date = {2014}, + langid = {english}, + note = {Publisher: Royal Society of Chemistry}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/3NZ9CIM4/Chance et al. - 2014 - The distribution of iodide at the sea surface.pdf:application/pdf}, +} + +@article{saiz-lopez_novel_2004, + title = {Novel iodine chemistry in the marine boundary layer}, + volume = {31}, + issn = {0094-8276}, + doi = {10.1029/2003GL019215}, + abstract = {The atmospheric chemistry of iodine is important for several reasons, including the influence of iodine oxides on the oxidising capacity of the troposphere, the formation of new particles, and the enrichment of iodine in marine aerosols and the transport of this essential dietary element to the continents. It is shown here that a substantial iodine source is I2, most likely emitted from macro-algae at low tide. This source accounts for the daytime production of new particles in the coastal marine boundary layer, and also explains the discovery of significant night-time levels of iodine oxides. Copyright 2004 by the American Geophysical Union.}, + pages = {L041121--4}, + number = {4}, + journaltitle = {Geophysical Research Letters}, + shortjournal = {Geophys. Res. Lett.}, + author = {Saiz-Lopez, Alfonso and Plane, John M.C.}, + date = {2004}, + note = {Publisher: American Geophysical Union}, + file = {Full Text:/Users/davidtschan/Zotero/storage/I4VMEQPY/Saiz-Lopez and Plane - 2004 - Novel iodine chemistry in the marine boundary layer.pdf:application/pdf;Snapshot:/Users/davidtschan/Zotero/storage/JALK7J3C/2542457420.html:text/html}, +} + +@article{mcfiggans_direct_2004, + title = {Direct evidence for coastal iodine particles from Laminaria macroalgae – linkage to emissions of molecular iodine}, + volume = {4}, + issn = {1680-7316}, + url = {https://acp.copernicus.org/articles/4/701/2004/}, + doi = {10.5194/acp-4-701-2004}, + abstract = {Renewal of ultrafine aerosols in the marine boundary layer may lead to repopulation of the marine distribution and ultimately determine the concentration of cloud condensation nuclei ({CCN}). Thus the formation of nanometre-scale particles can lead to enhanced scattering of incoming radiation and a net cooling of the atmosphere. The recent demonstration of the chamber formation of new particles from the photolytic production of condensable iodine-containing compounds from diiodomethane ({CH}2I2), (O'Dowd et al., 2002; Kolb, 2002; Jimenez et al., 2003a; Burkholder and Ravishankara, 2003), provides an additional mechanism to the gas-to-particle conversion of sulphuric acid formed in the photo-oxidation of dimethylsulphide for marine aerosol repopulation. {CH}2I2 is emitted from seaweeds (Carpenter et al., 1999, 2000) and has been suggested as an initiator of particle formation. We demonstrate here for the first time that ultrafine iodine-containing particles are produced by intertidal macroalgae exposed to ambient levels of ozone. The particle composition is very similar both to those formed in the chamber photo-oxidation of diiodomethane and in the oxidation of molecular iodine by ozone. The particles formed in all three systems are similarly aspherical. When small, those formed in the molecular iodine system swell only moderately when exposed to increased humidity environments, and swell progressively less with increasing size; this behaviour occurs whether they are formed in dry or humid environments, in contrast to those in the {CH}2I2 system. Direct coastal boundary layer observations of molecular iodine, ultrafine particle production and iodocarbons are reported. Using a newly measured molecular iodine photolysis rate, it is shown that, if atomic iodine is involved in the observed particle bursts, it is of the order of at least 1000 times more likely to result from molecular iodine photolysis than diiodomethane photolysis. A hypothesis for molecular iodine release from intertidal macroalgae is presented and the potential importance of macroalgal iodine particles in their contribution to {CCN} and global radiative forcing are discussed.}, + pages = {701--713}, + number = {3}, + journaltitle = {Atmospheric Chemistry and Physics}, + author = {{McFiggans}, G. and Coe, H. and Burgess, R. and Allan, J. and Cubison, M. and Alfarra, M. R. and Saunders, R. and Saiz-Lopez, A. and Plane, J. M. C. and Wevill, D. and Carpenter, L. and Rickard, A. R. and Monks, P. S.}, + urldate = {2025-12-12}, + date = {2004-05-07}, + note = {Publisher: Copernicus {GmbH}}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/ABXFEDJF/McFiggans et al. - 2004 - Direct evidence for coastal iodine particles from Laminaria macroalgae – linkage to emissions of mol.pdf:application/pdf}, +} + +@article{saiz-lopez_iodine_2014, + title = {Iodine chemistry in the troposphere and its effect on ozone}, + volume = {14}, + issn = {1680-7316}, + url = {https://acp.copernicus.org/articles/14/13119/2014/}, + doi = {10.5194/acp-14-13119-2014}, + abstract = {Despite the potential influence of iodine chemistry on the oxidizing capacity of the troposphere, reactive iodine distributions and their impact on tropospheric ozone remain almost unexplored aspects of the global atmosphere. Here we present a comprehensive global modelling experiment aimed at estimating lower and upper limits of the inorganic iodine burden and its impact on tropospheric ozone. Two sets of simulations without and with the photolysis of {IxOy} oxides (i.e. I2O2, I2O3 and I2O4) were conducted to define the range of inorganic iodine loading, partitioning and impact in the troposphere. Our results show that the most abundant daytime iodine species throughout the middle to upper troposphere is atomic iodine, with an annual average tropical abundance of (0.15–0.55) pptv. We propose the existence of a "tropical ring of atomic iodine" that peaks in the tropical upper troposphere ({\textasciitilde}11–14 km) at the equator and extends to the sub-tropics (30° N–30° S). Annual average daytime I / {IO} ratios larger than 3 are modelled within the tropics, reaching ratios up to {\textasciitilde}20 during vigorous uplift events within strong convective regions. We calculate that the integrated contribution of catalytic iodine reactions to the total rate of tropospheric ozone loss ({IOx} Loss) is 2–5 times larger than the combined bromine and chlorine cycles. When {IxOy} photolysis is included, {IOx} Loss represents an upper limit of approximately 27, 14 and 27\% of the tropical annual ozone loss for the marine boundary layer ({MBL}), free troposphere ({FT}) and upper troposphere ({UT}), respectively, while the lower limit throughout the tropical troposphere is {\textasciitilde}9\%. Our results indicate that iodine is the second strongest ozone-depleting family throughout the global marine {UT} and in the tropical {MBL}. We suggest that (i) iodine sources and its chemistry need to be included in global tropospheric chemistry models, (ii) experimental programs designed to quantify the iodine budget in the troposphere should include a strategy for the measurement of atomic I, and (iii) laboratory programs are needed to characterize the photochemistry of higher iodine oxides to determine their atmospheric fate since they can potentially dominate halogen-catalysed ozone destruction in the troposphere.}, + pages = {13119--13143}, + number = {23}, + journaltitle = {Atmospheric Chemistry and Physics}, + author = {Saiz-Lopez, A. and Fernandez, R. P. and Ordóñez, C. and Kinnison, D. E. and Gómez Martín, J. C. and Lamarque, J.-F. and Tilmes, S.}, + urldate = {2025-12-12}, + date = {2014-12-10}, + note = {Publisher: Copernicus {GmbH}}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/PGBFX2Z3/Saiz-Lopez et al. - 2014 - Iodine chemistry in the troposphere and its effect on ozone.pdf:application/pdf}, +} + +@article{hayase_heterogeneous_2010, + title = {Heterogeneous Reaction of Gaseous Ozone with Aqueous Iodide in the Presence of Aqueous Organic Species}, + volume = {114}, + issn = {1089-5639, 1520-5215}, + url = {https://pubs.acs.org/doi/10.1021/jp101985f}, + doi = {10.1021/jp101985f}, + pages = {6016--6021}, + number = {19}, + journaltitle = {The Journal of Physical Chemistry A}, + shortjournal = {J. Phys. Chem. A}, + author = {Hayase, Sayaka and Yabushita, Akihiro and Kawasaki, Masahiro and Enami, Shinichi and Hoffmann, Michael R. and Colussi, Agustín J.}, + urldate = {2025-12-15}, + date = {2010-05-20}, + langid = {english}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/MIGEZU6T/Hayase et al. - 2010 - Heterogeneous Reaction of Gaseous Ozone with Aqueous Iodide in the Presence of Aqueous Organic Speci.pdf:application/pdf}, +} + +@article{phillips_processes_2011, + title = {Processes at the gas–liquid interface}, + volume = {30}, + issn = {0144-235X}, + url = {https://doi.org/10.1080/0144235X.2011.611635}, + doi = {10.1080/0144235X.2011.611635}, + abstract = {Topics discussed in this article include: the structure of a gas–liquid interface; the nature of the small-scale motions of a liquid surface; a brief summary of some of the important results of beam experiments; the use of statistical mathematics to predict the efficiency of energy transfer during collisions of fast, light atoms with liquid surfaces, to account for the marked difference in energy transfer efficiency between ordinary liquids and liquid metals, and to predict the distribution of scattering angles for fast neon atoms striking a liquid surface; the application of Onsager's non-equilibrium thermodynamics to a gas–liquid interface; explanations for some paradoxical phenomena involving evaporation and condensation; experimental measurements of the Onsager heat of transport at the gas–liquid interface, and the significance of non-equilibrium thermodynamics in relation to air–sea exchange of carbon dioxide and global warming.}, + pages = {301--333}, + number = {3}, + journaltitle = {International Reviews in Physical Chemistry}, + author = {Phillips, Leon F.}, + urldate = {2025-12-16}, + date = {2011-07-01}, + note = {Publisher: Taylor \& Francis +\_eprint: https://doi.org/10.1080/0144235X.2011.611635}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/QIN6QSDK/Phillips - 2011 - Processes at the gas–liquid interface.pdf:application/pdf}, +} + +@article{davidovits_mass_2006, + title = {Mass Accommodation and Chemical Reactions at Gas−Liquid Interfaces}, + volume = {106}, + issn = {0009-2665, 1520-6890}, + url = {https://pubs.acs.org/doi/10.1021/cr040366k}, + doi = {10.1021/cr040366k}, + pages = {1323--1354}, + number = {4}, + journaltitle = {Chemical Reviews}, + shortjournal = {Chem. Rev.}, + author = {Davidovits, Paul and Kolb, Charles E. and Williams, Leah R. and Jayne, John T. and Worsnop, Douglas R.}, + urldate = {2025-12-16}, + date = {2006-04-01}, + langid = {english}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/J3LHXXG9/Davidovits et al. - 2006 - Mass Accommodation and Chemical Reactions at Gas−Liquid Interfaces.pdf:application/pdf}, +} + +@article{zheng_accelerated_2003, + title = {Accelerated Degradation of Methyl Iodide by Agrochemicals}, + volume = {51}, + issn = {0021-8561}, + url = {https://doi.org/10.1021/jf020820q}, + doi = {10.1021/jf020820q}, + abstract = {The fumigant methyl iodide ({MeI}, iodomethane) is considered a promising alternative to methyl bromide ({MeBr}) for soil-borne pest control in high-cash-value crops. However, the high vapor pressure of {MeI} results in emissions of a significant proportion of the applied mass into the ambient air, and this may lead to pollution of the environment. Integrating the application of certain agrochemicals with soil fumigation provides a novel approach to reduce excessive fumigant emissions. This study investigated the potential for several agrochemicals that are commonly used in farming operations, including fertilizers and nitrification inhibitors, to transform {MeI} in aqueous solution. The pseudo-first-order hydrolysis half-life (t1/2) of {MeI} was ∼108 d, while the transformation of {MeI} in aqueous solutions containing selected agrochemicals was more rapid, with t1/2 {\textless} 100 d (t1/2 {\textless} 0.5 d in some solutions containing nitrification inhibitors). The influence of these agrochemicals on the rate of {MeI} degradation in soil was also determined. Adsorption to soil apparently reduced the availability of some nitrification inhibitors in the soil aqueous phase and lowered the degradation rate in soil. In contrast, addition of the nitrification inhibitors thiourea and allylthiourea to soil significantly accelerated the degradation of {MeI}, possibly due to soil surface catalysis. The t1/2 of {MeI} was {\textless}20 h in thiourea- and allylthiourea-amended soil, considerably less than that in unamended soil (t1/2 {\textgreater} 300 h). Keywords: {MeI}; methyl iodide; iodomethane; degradation; transformation; nitrification inhibitor; fertilizer; soil; agrochemical}, + pages = {673--679}, + number = {3}, + journaltitle = {Journal of Agricultural and Food Chemistry}, + shortjournal = {J. Agric. Food Chem.}, + author = {Zheng, Wei and Papiernik, Sharon K. and Guo, Mingxin and Yates, Scott R.}, + urldate = {2025-12-16}, + date = {2003-01-01}, + note = {Publisher: American Chemical Society}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/NS7UZQE2/Zheng et al. - 2003 - Accelerated Degradation of Methyl Iodide by Agrochemicals.pdf:application/pdf}, +} + +@article{carpenter_marine_2021, + title = {Marine iodine emissions in a changing world}, + volume = {477}, + issn = {1364-5021, 1471-2946}, + url = {https://royalsocietypublishing.org/doi/10.1098/rspa.2020.0824}, + doi = {10.1098/rspa.2020.0824}, + abstract = {Iodine is a critical trace element involved in many diverse and important processes in the Earth system. The importance of iodine for human health has been known for over a century, with low iodine in the diet being linked to goitre, cretinism and neonatal death. Research over the last few decades has shown that iodine has significant impacts on tropospheric photochemistry, ultimately impacting climate by reducing the radiative forcing of ozone (O + 3 + ) and air quality by reducing extreme O + 3 + concentrations in polluted regions. Iodine is naturally present in the ocean, predominantly as aqueous iodide and iodate. The rapid reaction of sea-surface iodide with O + 3 + is believed to be the largest single source of gaseous iodine to the atmosphere. Due to increased anthropogenic O + 3 + , this release of iodine is believed to have increased dramatically over the twentieth century, by as much as a factor of 3. Uncertainties in the marine iodine distribution and global cycle are, however, major constraints in the effective prediction of how the emissions of iodine and its biogeochemical cycle may change in the future or have changed in the past. Here, we present a synthesis of recent results by our team and others which bring a fresh perspective to understanding the global iodine biogeochemical cycle. In particular, we suggest that future climate-induced oceanographic changes could result in a significant change in aqueous iodide concentrations in the surface ocean, with implications for atmospheric air quality and climate.}, + pages = {20200824}, + number = {2247}, + journaltitle = {Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences}, + shortjournal = {Proc. R. Soc. A.}, + author = {Carpenter, Lucy J. and Chance, Rosie J. and Sherwen, Tomás and Adams, Thomas J. and Ball, Stephen M. and Evans, Mat J. and Hepach, Helmke and Hollis, Lloyd D. J. and Hughes, Claire and Jickells, Timothy D. and Mahajan, Anoop and Stevens, David P. and Tinel, Liselotte and Wadley, Martin R.}, + urldate = {2025-12-16}, + date = {2021-03}, + langid = {english}, + file = {PDF:/Users/davidtschan/Zotero/storage/H45P9KNU/Carpenter et al. - 2021 - Marine iodine emissions in a changing world.pdf:application/pdf}, +} + +@article{giese_release_1999, + title = {Release of Volatile Iodinated C$_{\textrm{1}}$ −C$_{\textrm{4}}$ Hydrocarbons by Marine Macroalgae from Various Climate Zones}, + volume = {33}, + issn = {0013-936X, 1520-5851}, + url = {https://pubs.acs.org/doi/10.1021/es980731n}, + doi = {10.1021/es980731n}, + pages = {2432--2439}, + number = {14}, + journaltitle = {Environmental Science \& Technology}, + shortjournal = {Environ. Sci. Technol.}, + author = {Giese, Bernd and Laturnus, Frank and Adams, Freddy C. and Wiencke, Christian}, + urldate = {2025-12-16}, + date = {1999-07-01}, + langid = {english}, + keywords = {Unread}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/VUE6ZHRZ/Giese et al. - 1999 - Release of Volatile Iodinated C1 −C4 Hydrocarbons by Marine Macroalgae from Va.pdf:application/pdf}, +} + +@article{chuck_oceanic_2005, + title = {Oceanic distributions and air-sea fluxes of biogenic halocarbons in the open ocean}, + volume = {110}, + rights = {Copyright 2005 by the American Geophysical Union.}, + issn = {2156-2202}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1029/2004JC002741}, + doi = {10.1029/2004JC002741}, + abstract = {Surface seawater and atmospheric concentrations of methyl iodide, chloroiodomethane, bromoform, dichlorobromomethane, and chlorodibromethane were measured during three open ocean cruises in the Atlantic and Southern oceans. The measurements spanned a longitudinal range of 115°, between 50°N and 65°S. The saturation anomalies and the instantaneous air-sea fluxes of the gases during one of these cruises ({ANT} {XVIII}/1) are presented and discussed. Methyl iodide and chloroiodomethane were highly supersaturated ({\textgreater}1000\%) throughout the temperate and tropical regions, with calculated mean fluxes of 15 and 5.5 nmol m−2 d−1, respectively. The oceanic emissions of the brominated compounds were less substantial, and a significant area of the temperate Atlantic Ocean was found to be a sink for bromoform. Correlation analyses have been used to investigate possible controls on the concentrations of these gases. In particular, the relationship of {CH}3I with sea surface temperature and light is discussed, with the tentative conclusion that this compound may be formed abiotically.}, + issue = {C10}, + journaltitle = {Journal of Geophysical Research: Oceans}, + author = {Chuck, Adele L. and Turner, Suzanne M. and Liss, Peter S.}, + urldate = {2025-12-16}, + date = {2005}, + langid = {english}, + note = {\_eprint: https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2004JC002741}, + keywords = {bromoform, halocarbons, Atlantic Ocean, methyl iodide, trace gases}, + file = {PDF:/Users/davidtschan/Zotero/storage/7WHBJ76R/Chuck et al. - 2005 - Oceanic distributions and air-sea fluxes of biogenic halocarbons in the open ocean.pdf:application/pdf;Snapshot:/Users/davidtschan/Zotero/storage/BBWUENTK/2004JC002741.html:text/html}, +} + +@article{archer_marked_2007, + title = {Marked seasonality in the concentrations and sea-to-air flux of volatile iodocarbon compounds in the western English Channel}, + volume = {112}, + rights = {Copyright 2007 by the American Geophysical Union.}, + issn = {2156-2202}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1029/2006JC003963}, + doi = {10.1029/2006JC003963}, + abstract = {In the first seasonal study of volatile iodinated organic compounds ({VICs}) in the open sea, concentrations of five {VICs} were measured approximately weekly at four depths, over 20 months from July 2002 to April 2004, in the western English Channel. Seawater concentrations varied seasonally by an order of magnitude for all five compounds, with winter minima and, generally, late summer/autumn maxima. The average contribution to the dissolved {VIC} pool was chloroiodomethane (39\%), diiodomethane (33\%), iodomethane (22\%), iodoethane (6\%), and bromoiodomethane (4\%). Total sea-to-air flux of iodine atoms carried by the {VICs} (15.5 μmol I m−2 yr−1) was approximately fourfold higher than that for iodomethane alone. This contrasts with previous studies that indicated that iodomethane was the main vector of iodine away from macroalgal beds. The estimated sea-to-air flux takes into account the significant airside control of the gas exchange of certain {VICs}, particularly diiodomethane; for which a 30\% reduction in average daily flux was observed when an additional airside transfer velocity was included in the calculations. Because of their high reactivity, chloroiodomethane and diiodomethane are likely to drive the atmospheric organic iodine chemistry over these shelf seas, rather than the monohalogenated {VICs}.}, + issue = {C8}, + journaltitle = {Journal of Geophysical Research: Oceans}, + author = {Archer, Stephen D. and Goldson, Laura E. and Liddicoat, Malcolm I. and Cummings, Denise G. and Nightingale, Philip D.}, + urldate = {2025-12-16}, + date = {2007}, + langid = {english}, + note = {\_eprint: https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2006JC003963}, + keywords = {seawater, Iodocarbon, seasonal}, + file = {Full Text:/Users/davidtschan/Zotero/storage/ITDPAKKV/Archer et al. - 2007 - Marked seasonality in the concentrations and sea-to-air flux of volatile iodocarbon compounds in the.pdf:application/pdf;Snapshot:/Users/davidtschan/Zotero/storage/MYGDDIN8/2006JC003963.html:text/html}, +} + +@article{hou_review_2009, + title = {A review on speciation of iodine-129 in the environmental and biological samples}, + volume = {632}, + issn = {00032670}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S0003267008019211}, + doi = {10.1016/j.aca.2008.11.013}, + abstract = {As a long-lived beta-emitting radioisotope of iodine, 129I is produced both naturally and as a result of human nuclear activities. At present time, the main part of 129I in the environment originates from the human nuclear activity, especially the releases from the spent nuclear fuel reprocessing plants, the 129I/127I ratios have being reached to values of 10−10 to 10−4 in the environment from 10−12 in the pre-nuclear era. In this article, we review the occurrence, sources, inventory, and concentration level of 129I in environment and the method for speciation analysis of 129I in the environment. Measurement techniques for the determination of 129I are presented and compared. An overview of applications of 129I speciation in various scientific disciplines such as radiation protection, waste depository, and environmental sciences is given. In addition, the bioavailability and radiation toxicity (dose to thyroid) of 129I are discussed.}, + pages = {181--196}, + number = {2}, + journaltitle = {Analytica Chimica Acta}, + shortjournal = {Analytica Chimica Acta}, + author = {Hou, Xiaolin and Hansen, Violeta and Aldahan, Ala and Possnert, Göran and Lind, Ole Christian and Lujaniene, Galina}, + urldate = {2025-12-16}, + date = {2009-01}, + langid = {english}, + file = {PDF:/Users/davidtschan/Zotero/storage/HUUBJI2G/Hou et al. - 2009 - A review on speciation of iodine-129 in the environmental and biological samples.pdf:application/pdf}, +} + +@article{dillon_absorption_2005, + title = {Absorption cross-section of {IO} at 427.2 nm and 298 K}, + volume = {176}, + issn = {10106030}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S101060300500465X}, + doi = {10.1016/j.jphotochem.2005.09.025}, + abstract = {The absorption cross-section of the {IO} radical was determined at a wavelength of 427.2 nm and at a resolution of ≈0.08 nm at room temperature (298 ± 2 K) using the technique of laser photolysis combined with transient absorption spectroscopy. Three previously untested chemical schemes were used to generate calibrated amounts of {IO} and two of these were used to derive a cross-section of σ4I2O7.2 nm = (3.55 ± 0.35) × 10−7 cm2 molecule−1. The value of σmax, at the peak of the 4,0 band (located at ≈427.08 nm, wavelengths given in air) is ≈8\% larger than at 427.2 nm. This result is compared with previous determinations and evaluations. As part of this study the branching ratio (at 298 K) of {IO} formation from the reactions of O(3P) with {CF}3I and {CH}3I were measured as 0.90 ± 0.05 and 0.38 ± 0.05, respectively. Data on the formation and relaxation of vibrationally excited {IO} in the chemical systems used in this study were also obtained.}, + pages = {3--14}, + number = {1}, + journaltitle = {Journal of Photochemistry and Photobiology A: Chemistry}, + shortjournal = {Journal of Photochemistry and Photobiology A: Chemistry}, + author = {Dillon, T.J. and Tucceri, M.E. and Hölscher, D. and Crowley, J.N.}, + urldate = {2025-12-16}, + date = {2005-12}, + langid = {english}, + file = {PDF:/Users/davidtschan/Zotero/storage/XXTLCYCK/Dillon et al. - 2005 - Absorption cross-section of IO at 427.2 nm and 298 K.pdf:application/pdf}, +} + +@article{hong_methylmercury_2012, + title = {Methylmercury Exposure and Health Effects}, + volume = {45}, + issn = {1975-8375}, + url = {https://pmc.ncbi.nlm.nih.gov/articles/PMC3514465/}, + doi = {10.3961/jpmph.2012.45.6.353}, + abstract = {Methylmercury is a hazardous substance that is of interest with regard to environmental health, as inorganic mercury circulating in the general environment is dissolved into freshwater and seawater, condensed through the food chain, ingested by humans, and consequently affects human health. Recently, there has been much interest and discussion regarding the toxicity of methylmercury, the correlation with fish and shellfish intake, and methods of long-term management of the human health effects of methylmercury. What effects chronic exposure to a low concentration of methylmercury has on human health remains controversial. Although the possibility of methylmercury poisoning the heart and blood vessel system, the reproductive system, and the immune system is continuously raised and discussed, and the carcinogenicity of methylmercury is also under discussion, a clear conclusion regarding the human health effects according to exposure level has not yet been drawn. The Joint {FAO}/{WHO} Expert Committee on Food Additives proposed to prepare additional fish and shellfish intake recommendations for consumers based on the quantified evaluation of the hazardousness of methylmercury contained in fish and shellfish, methylmercury management in the Korea has not yet caught up with this international trend. Currently, the methylmercury exposure level of Koreans is known to be very high. The starting point of methylmercury exposure management is inorganic mercury in the general environment, but food intake through methylation is the main exposure source. Along with efforts to reduce mercury in the general environment, food intake management should be undertaken to reduce the human exposure to methylmercury in Korea.}, + pages = {353--363}, + number = {6}, + journaltitle = {Journal of Preventive Medicine and Public Health}, + shortjournal = {J Prev Med Public Health}, + author = {Hong, Young-Seoub and Kim, Yu-Mi and Lee, Kyung-Eun}, + urldate = {2025-12-17}, + date = {2012-11}, + pmid = {23230465}, + pmcid = {PMC3514465}, + file = {Full Text:/Users/davidtschan/Zotero/storage/3GIXJWGS/Hong et al. - 2012 - Methylmercury Exposure and Health Effects.pdf:application/pdf}, +} + +@article{scheuhammer_effects_2007, + title = {Effects of Environmental Methylmercury on the Health of Wild Birds, Mammals, and Fish}, + volume = {36}, + issn = {0044-7447, 1654-7209}, + url = {https://bioone.org/journals/ambio-a-journal-of-the-human-environment/volume-36/issue-1/0044-7447_2007_36_12_EOEMOT_2.0.CO_2/Effects-of-Environmental-Methylmercury-on-the-Health-of-Wild-Birds/10.1579/0044-7447(2007)36[12:EOEMOT]2.0.CO;2.full}, + doi = {10.1579/0044-7447(2007)36[12:EOEMOT]2.0.CO;2}, + abstract = {Wild piscivorous fish, mammals, and birds may be at risk for elevated dietary methylmercury intake and toxicity. In controlled feeding studies, the consumption of diets that contained Hg (as methylmercury) at environmentally realistic concentrations resulted in a range of toxic effects in fish, birds, and mammals, including behavioral, neurochemical, hormonal, and reproductive changes. Limited field-based studies, especially with certain wild piscivorous bird species, e.g., the common loon, corroborated laboratory-based results, demonstrating significant relations between methylmercury exposure and various indicators of methylmercury toxicity, including reproductive impairment. Potential population effects in fish and wildlife resulting from dietary methylmercury exposure are expected to vary as a function of species life history, as well as regional differences in fish-Hg concentrations, which, in turn, are influenced by differences in Hg deposition and environmental methylation rates. However, population modeling suggests that reductions in Hg emissions could have substantial benefits for some common loon populations that are currently experiencing elevated methylmercury exposure. Predicted benefits would be mediated primarily through improved hatching success and development of hatchlings to maturity as Hg concentrations in prey fish decline. Other piscivorous species may also benefit from decreased Hg exposure but have not been as extensively studied as the common loon.}, + pages = {12--19}, + number = {1}, + journaltitle = {{AMBIO}: A Journal of the Human Environment}, + shortjournal = {ambi}, + author = {Scheuhammer, Anton M. and Meyer, Michael W. and Sandheinrich, Mark B. and Murray, Michael W.}, + urldate = {2025-12-17}, + date = {2007-02}, + note = {Publisher: Royal Swedish Academy of Sciences}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/SV3547VS/Scheuhammer et al. - 2007 - Effects of Environmental Methylmercury on the Health of Wild Birds, Mammals, and Fish.pdf:application/pdf}, +} + +@article{steffen_synthesis_2008, + title = {A synthesis of atmospheric mercury depletion event chemistry in the atmosphere and snow}, + volume = {8}, + issn = {1680-7316}, + url = {https://acp.copernicus.org/articles/8/1445/2008/acp-8-1445-2008.html}, + doi = {10.5194/acp-8-1445-2008}, + abstract = {It was discovered in 1995 that, during the spring time, unexpectedly low concentrations of gaseous elemental mercury ({GEM}) occurred in the Arctic air. This was surprising for a pollutant known to have a long residence time in the atmosphere; however conditions appeared to exist in the Arctic that promoted this depletion of mercury (Hg). This phenomenon is termed atmospheric mercury depletion events ({AMDEs}) and its discovery has revolutionized our understanding of the cycling of Hg in Polar Regions while stimulating a significant amount of research to understand its impact to this fragile ecosystem. Shortly after the discovery was made in Canada, {AMDEs} were confirmed to occur throughout the Arctic, sub-Artic and Antarctic coasts. It is now known that, through a series of photochemically initiated reactions involving halogens, {GEM} is converted to a more reactive species and is subsequently associated to particles in the air and/or deposited to the polar environment. {AMDEs} are a means by which Hg is transferred from the atmosphere to the environment that was previously unknown. In this article we review Hg research taken place in Polar Regions pertaining to {AMDEs}, the methods used to collect Hg in different environmental media, research results of the current understanding of {AMDEs} from field, laboratory and modeling work, how Hg cycles around the environment after {AMDEs}, gaps in our current knowledge and the future impacts that {AMDEs} may have on polar environments. The research presented has shown that while considerable improvements in methodology to measure Hg have been made but the main limitation remains knowing the speciation of Hg in the various media. The processes that drive {AMDEs} and how they occur are discussed. As well, the role that the snow pack and the sea ice play in the cycling of Hg is presented. It has been found that deposition of Hg from {AMDEs} occurs at marine coasts and not far inland and that a fraction of the deposited Hg does not remain in the same form in the snow. Kinetic studies undertaken have demonstrated that bromine is the major oxidant depleting Hg in the atmosphere. Modeling results demonstrate that there is a significant deposition of Hg to Polar Regions as a result of {AMDEs}. Models have also shown that Hg is readily transported to the Arctic from source regions, at times during springtime when this environment is actively transforming Hg from the atmosphere to the snow and ice surfaces. The presence of significant amounts of methyl Hg in snow in the Arctic surrounding {AMDEs} is important because this species is the link between the environment and impacts to wildlife and humans. Further, much work on methylation and demethylation processes has occurred but these processes are not yet fully understood. Recent changes in the climate and sea ice cover in Polar Regions are likely to have strong effects on the cycling of Hg in this environment; however more research is needed to understand Hg processes in order to formulate meaningful predictions of these changes.}, + pages = {1445--1482}, + number = {6}, + journaltitle = {Atmospheric Chemistry and Physics}, + author = {Steffen, A. and Douglas, T. and Amyot, M. and Ariya, P. and Aspmo, K. and Berg, T. and Bottenheim, J. and Brooks, S. and Cobbett, F. and Dastoor, A. and Dommergue, A. and Ebinghaus, R. and Ferrari, C. and Gardfeldt, K. and Goodsite, M. E. and Lean, D. and Poulain, A. J. and Scherz, C. and Skov, H. and Sommar, J. and Temme, C.}, + urldate = {2025-12-17}, + date = {2008-03-12}, + note = {Publisher: Copernicus {GmbH}}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/56Z7Y4IA/Steffen et al. - 2008 - A synthesis of atmospheric mercury depletion event chemistry in the atmosphere and snow.pdf:application/pdf}, +} + +@article{simpson_halogens_2007, + title = {Halogens and their role in polar boundary-layer ozone depletion}, + volume = {7}, + issn = {1680-7316}, + url = {https://acp.copernicus.org/articles/7/4375/2007/}, + doi = {10.5194/acp-7-4375-2007}, + abstract = {During springtime in the polar regions, unique photochemistry converts inert halide salt ions (e.g. Br\−) into reactive halogen species (e.g. Br atoms and {BrO}) that deplete ozone in the boundary layer to near zero levels. Since their discovery in the late 1980s, research on ozone depletion events ({ODEs}) has made great advances; however many key processes remain poorly understood. In this article we review the history, chemistry, dependence on environmental conditions, and impacts of {ODEs}. This research has shown the central role of bromine photochemistry, but how salts are transported from the ocean and are oxidized to become reactive halogen species in the air is still not fully understood. Halogens other than bromine (chlorine and iodine) are also activated through incompletely understood mechanisms that are probably coupled to bromine chemistry. The main consequence of halogen activation is chemical destruction of ozone, which removes the primary precursor of atmospheric oxidation, and generation of reactive halogen atoms/oxides that become the primary oxidizing species. The different reactivity of halogens as compared to {OH} and ozone has broad impacts on atmospheric chemistry, including near complete removal and deposition of mercury, alteration of oxidation fates for organic gases, and export of bromine into the free troposphere. Recent changes in the climate of the Arctic and state of the Arctic sea ice cover are likely to have strong effects on halogen activation and {ODEs}; however, more research is needed to make meaningful predictions of these changes.}, + pages = {4375--4418}, + number = {16}, + journaltitle = {Atmospheric Chemistry and Physics}, + author = {Simpson, W. R. and von Glasow, R. and Riedel, K. and Anderson, P. and Ariya, P. and Bottenheim, J. and Burrows, J. and Carpenter, L. J. and Frieß, U. and Goodsite, M. E. and Heard, D. and Hutterli, M. and Jacobi, H.-W. and Kaleschke, L. and Neff, B. and Plane, J. and Platt, U. and Richter, A. and Roscoe, H. and Sander, R. and Shepson, P. and Sodeau, J. and Steffen, A. and Wagner, T. and Wolff, E.}, + urldate = {2025-12-17}, + date = {2007-08-22}, + note = {Publisher: Copernicus {GmbH}}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/C3PNRVL5/Simpson et al. - 2007 - Halogens and their role in polar boundary-layer ozone depletion.pdf:application/pdf}, +} + +@article{moore_bromoperoxidase_1996, + title = {Bromoperoxidase and iodoperoxidase enzymes and production of halogenated methanes in marine diatom cultures}, + volume = {101}, + rights = {Copyright 1996 by the American Geophysical Union.}, + issn = {2156-2202}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1029/96JC01248}, + doi = {10.1029/96JC01248}, + abstract = {Halogenated methanes produced in the oceans are important as carriers of chlorine, bromine, and iodine into the atmosphere. There they play roles in the regulation of ozone in the stratosphere and perhaps in the Arctic troposphere at polar sunrise. While the mechanisms for the production of some polyhalogenated compounds by marine macrophytes have previously been substantially elucidated, the same has not been true in the case of marine phytoplankton. We describe laboratory experiments on the production of various brominated and iodinated compounds in cultures of marine diatoms, obtained from the Provasoli-Guillard Center for Culture of Marine Phytoplankton collections (Bigelow Laboratory for Ocean Sciences, Maine, {USA}; {CCMP}). Species examined included Nitzschia sp. ({CCMP} 580), Nitzschia arctica, Porosira glacialis, and two Navicula sp. ({CCMP} 545 and 546). A suite of brominated compounds, notably bromoform and dibromomethane, is produced by the Nitzschia and Porosira species. Nitzschia sp.({CCMP} 580) was grown in sufficient quantities to allow the identification of a bromoperoxidase enzyme, which is assumed to be responsible not only for the {CHBr}3 and {CH}2Br2 production but also for {CH}2I2 which was measured in those cultures. Chloroiodomethane was produced, either directly by the algae or by a photochemical reaction of {CH}2I2. One Navicula species ({CCMP} 545), found to produce {CH}2I2 and {CH}2ClI, was shown to possess an iodoperoxidase. Bromoform and dibromomethane were not detected in cultures of this species. Other compounds produced in certain of these non axenic cultures included methyl and ethyl iodide, and bromoiodomethane.}, + pages = {20899--20908}, + issue = {C9}, + journaltitle = {Journal of Geophysical Research: Oceans}, + author = {Moore, R. M. and Webb, M. and Tokarczyk, R. and Wever, R.}, + urldate = {2025-12-18}, + date = {1996}, + langid = {english}, + note = {\_eprint: https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/96JC01248}, + file = {PDF:/Users/davidtschan/Zotero/storage/55SAUKPU/Moore et al. - 1996 - Bromoperoxidase and iodoperoxidase enzymes and production of halogenated methanes in marine diatom c.pdf:application/pdf}, +} + +@article{lovelock_halogenated_1973, + title = {Halogenated Hydrocarbons in and over the Atlantic}, + volume = {241}, + rights = {1973 Springer Nature Limited}, + issn = {1476-4687}, + url = {https://www.nature.com/articles/241194a0}, + doi = {10.1038/241194a0}, + abstract = {{DURING} the past few decades the production of the chlorofluorocarbons, the propellant solvents for aerosol dispensers, has grown exponentially. R. L. {McCarthy} (unpublished) estimates that the integrated production of {CCl}2F2 and of {CCl}3F, the two principal compounds of the class, was about one megaton of each in mid 1971; they are unusually stable chemically and only slightly soluble in water and might therefore persist and accumulate in the atmosphere. Preliminary tests in 1970 showed that {CCl}3F was present in the air over Ireland at concentrations exceeding 10−11 by volume1.}, + pages = {194--196}, + number = {5386}, + journaltitle = {Nature}, + author = {Lovelock, J. E. and Maggs, R. J. and Wade, R. J.}, + urldate = {2025-12-18}, + date = {1973-01}, + langid = {english}, + note = {Publisher: Nature Publishing Group}, + keywords = {Humanities and Social Sciences, multidisciplinary, Science}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/7I9EKGFJ/Lovelock et al. - 1973 - Halogenated Hydrocarbons in and over the Atlantic.pdf:application/pdf}, +} + +@article{wuosmaa_methyl_1990, + title = {Methyl Chloride Transferase: a Carbocation Route for Biosynthesis of Halometabolites}, + volume = {249}, + url = {https://www.science.org/doi/abs/10.1126/science.2371563}, + doi = {10.1126/science.2371563}, + shorttitle = {Methyl Chloride Transferase}, + abstract = {Enzymatic synthesis of methyl halides through an S-adenosyl methionine transfer mechanism has been detected in cell extracts of Phellinus promaceus (a white rot fungus), Endocladia muricata (a marine red algae), and Mesembryanthemum crystallium (ice plant). This mechanism represents a novel pathway for the formation of halometabolites. The Michaelis constants for chloride and bromide ion and for S-adenosyl methionine in the reaction have been determined for the enzyme from E. muricata. A recent survey of marine algae indicates that there may be a broad distribution of this enzyme among marine algae.}, + pages = {160--162}, + number = {4965}, + journaltitle = {Science}, + author = {Wuosmaa, Anne Marie and Hager, Lowell P.}, + urldate = {2025-12-18}, + date = {1990-07-13}, + note = {Publisher: American Association for the Advancement of Science}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/CNH9E2I7/Wuosmaa and Hager - 1990 - Methyl Chloride Transferase a Carbocation Route for Biosynthesis of Halometabolites.pdf:application/pdf}, +} + +@article{butler_role_nodate, + title = {The role of vanadium bromoperoxidase in the biosynthesis of halogenated marine natural products}, + journaltitle = {Nat. Prod. Rep.}, + author = {Butler, Alison and Carter-Franklin, Jayme N}, + langid = {english}, + file = {PDF:/Users/davidtschan/Zotero/storage/IPHIJ29S/Butler and Carter-Franklin - The role of vanadium bromoperoxidase in the biosynthesis of halogenated marine natural products.pdf:application/pdf}, +} + +@article{soedjak_inhibition_1995, + title = {Inhibition and inactivation of vanadium bromoperoxidase by the substrate hydrogen peroxide and further mechanistic studies}, + volume = {34}, + issn = {0006-2960, 1520-4995}, + url = {https://pubs.acs.org/doi/abs/10.1021/bi00039a027}, + doi = {10.1021/bi00039a027}, + pages = {12689--12696}, + number = {39}, + journaltitle = {Biochemistry}, + shortjournal = {Biochemistry}, + author = {Soedjak, Helena S. and Walker, J. V. and Butler, Alison}, + urldate = {2025-12-18}, + date = {1995-10-03}, + langid = {english}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/7B2KV725/Soedjak et al. - 1995 - Inhibition and inactivation of vanadium bromoperoxidase by the substrate hydrogen peroxide and furth.pdf:application/pdf}, +} + +@article{zhang_samsah_2016, + title = {{SAM}/{SAH} Analogs as Versatile Tools for {SAM}-Dependent Methyltransferases}, + volume = {11}, + issn = {1554-8929, 1554-8937}, + url = {https://pubs.acs.org/doi/10.1021/acschembio.5b00812}, + doi = {10.1021/acschembio.5b00812}, + pages = {583--597}, + number = {3}, + journaltitle = {{ACS} Chemical Biology}, + shortjournal = {{ACS} Chem. Biol.}, + author = {Zhang, Jing and Zheng, Yujun George}, + urldate = {2025-12-18}, + date = {2016-03-18}, + langid = {english}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/MUXFIEBV/Zhang and Zheng - 2016 - SAMSAH Analogs as Versatile Tools for SAM-Dependent Methyltransferases.pdf:application/pdf}, +} + +@article{fontecave_s-adenosylmethionine_2004, + title = {S-adenosylmethionine: nothing goes to waste}, + volume = {29}, + issn = {0968-0004}, + url = {https://www.cell.com/trends/biochemical-sciences/abstract/S0968-0004(04)00075-1}, + doi = {10.1016/j.tibs.2004.03.007}, + shorttitle = {S-adenosylmethionine}, + pages = {243--249}, + number = {5}, + journaltitle = {Trends in Biochemical Sciences}, + shortjournal = {Trends in Biochemical Sciences}, + author = {Fontecave, Marc and Atta, Mohamed and Mulliez, Etienne}, + urldate = {2025-12-18}, + date = {2004-05-01}, + pmid = {15130560}, + note = {Publisher: Elsevier}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/7I2EIW47/Fontecave et al. - 2004 - S-adenosylmethionine nothing goes to waste.pdf:application/pdf}, +} + +@article{zeides_unraveling_2025, + title = {Unraveling the molecular basis of substrate specificity and halogen activation in vanadium-dependent haloperoxidases}, + volume = {16}, + rights = {2025 The Author(s)}, + issn = {2041-1723}, + url = {https://www.nature.com/articles/s41467-025-57023-1}, + doi = {10.1038/s41467-025-57023-1}, + abstract = {Vanadium-dependent haloperoxidases ({VHPOs}) are biotechnologically valuable and operationally versatile biocatalysts. {VHPOs} share remarkable active-site structural similarities yet display variable reactivity and selectivity. The factors dictating substrate specificity and, thus, a general understanding of {VHPO} reaction control still need to be discovered. This work’s strategic single-point mutation in the cyanobacterial bromoperoxidase {AmVHPO} facilitates a selectivity switch to allow aryl chlorination. This mutation induces loop formation that interacts with the neighboring protein monomer, creating a tunnel to the active sites. Structural analysis of the substrate-R425S-mutant complex reveals a substrate-binding site at the interface of two adjacent units. There, residues Glu139 and Phe401 interact with arenes, extending the substrate residence time close to the vanadate cofactor and stabilizing intermediates. Our findings validate the long-debated existence of direct substrate binding and provide a detailed {VHPO} mechanistic understanding. This work will pave the way for a broader application of {VHPOs} in diverse chemical processes.}, + pages = {2083}, + number = {1}, + journaltitle = {Nature Communications}, + shortjournal = {Nat Commun}, + author = {Zeides, P. and Bellmann-Sickert, K. and Zhang, Ru and Seel, C. J. and Most, V. and Schoeder, C. T. and Groll, M. and Gulder, T.}, + urldate = {2025-12-18}, + date = {2025-02-28}, + langid = {english}, + note = {Publisher: Nature Publishing Group}, + keywords = {Biocatalysis, Enzyme mechanisms, Enzymes, Reaction mechanisms, X-ray crystallography}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/25LY9VR2/Zeides et al. - 2025 - Unraveling the molecular basis of substrate specificity and halogen activation in vanadium-dependent.pdf:application/pdf}, +} + +@article{butler_mechanistic_2009, + title = {Mechanistic considerations of halogenating enzymes}, + volume = {460}, + rights = {2009 Springer Nature Limited}, + issn = {1476-4687}, + url = {https://www.nature.com/articles/nature08303}, + doi = {10.1038/nature08303}, + abstract = {In nature, halogenation is a strategy used to increase the biological activity of secondary metabolites, compounds that are often effective as drugs. However, halides are not particularly reactive unless they are activated, typically by oxidation. The pace of discovery of new enzymes for halogenation is increasing, revealing new metalloenzymes, flavoenzymes, S-adenosyl-L-methionine ({SAM})-dependent enzymes and others that catalyse halide oxidation using dioxygen, hydrogen peroxide and hydroperoxides, or that promote nucleophilic halide addition reactions.}, + pages = {848--854}, + number = {7257}, + journaltitle = {Nature}, + author = {Butler, Alison and Sandy, Moriah}, + urldate = {2025-12-18}, + date = {2009-08}, + langid = {english}, + note = {Publisher: Nature Publishing Group}, + keywords = {Humanities and Social Sciences, multidisciplinary, Science}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/JFCQXFUV/Butler and Sandy - 2009 - Mechanistic considerations of halogenating enzymes.pdf:application/pdf}, +} + +@article{agarwal_enzymatic_2017, + title = {Enzymatic Halogenation and Dehalogenation Reactions: Pervasive and Mechanistically Diverse}, + volume = {117}, + issn = {0009-2665, 1520-6890}, + url = {https://pubs.acs.org/doi/10.1021/acs.chemrev.6b00571}, + doi = {10.1021/acs.chemrev.6b00571}, + shorttitle = {Enzymatic Halogenation and Dehalogenation Reactions}, + pages = {5619--5674}, + number = {8}, + journaltitle = {Chemical Reviews}, + shortjournal = {Chem. Rev.}, + author = {Agarwal, Vinayak and Miles, Zachary D. and Winter, Jaclyn M. and Eustáquio, Alessandra S. and El Gamal, Abrahim A. and Moore, Bradley S.}, + urldate = {2025-12-18}, + date = {2017-04-26}, + langid = {english}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/CHH4WLHK/Agarwal et al. - 2017 - Enzymatic Halogenation and Dehalogenation Reactions Pervasive and Mechanistically Diverse.pdf:application/pdf}, +} + +@article{hemrika_heterologous_1999, + title = {Heterologous Expression of the Vanadium-containing Chloroperoxidase from Curvularia inaequalis in Saccharomyces cerevisiae and Site-directed Mutagenesis of the Active Site Residues His496, Lys353, Arg360, and Arg490}, + volume = {274}, + rights = {https://www.elsevier.com/tdm/userlicense/1.0/}, + issn = {00219258}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S0021925819554977}, + doi = {10.1074/jbc.274.34.23820}, + pages = {23820--23827}, + number = {34}, + journaltitle = {Journal of Biological Chemistry}, + shortjournal = {Journal of Biological Chemistry}, + author = {Hemrika, Wieger and Renirie, Rokus and Macedo-Ribeiro, Sandra and Messerschmidt, Albrecht and Wever, Ron}, + urldate = {2025-12-18}, + date = {1999-08}, + langid = {english}, + file = {PDF:/Users/davidtschan/Zotero/storage/EHS8BGMF/Hemrika et al. - 1999 - Heterologous Expression of the Vanadium-containing Chloroperoxidase from Curvularia inaequalis in Sa.pdf:application/pdf}, +} + +@article{renirie_peroxidase_2000, + title = {Peroxidase and Phosphatase Activity of Active-site Mutants of Vanadium Chloroperoxidase from the Fungus \textit{Curvularia inaequalis}}, + volume = {275}, + issn = {0021-9258}, + url = {https://www.sciencedirect.com/science/article/pii/S0021925819808001}, + doi = {10.1074/jbc.275.16.11650}, + abstract = {Mutation studies were performed on active-site residues of vanadium chloroperoxidase from the fungus Curvularia inaequalis, an enzyme which exhibits both haloperoxidase and phosphatase activity and is related to glucose-6-phosphatase. The effects of mutation to alanine on haloperoxidase activity were studied for the proposed catalytic residue His-404 and for residue Asp-292, which is located close to the vanadate cofactor. The mutants were strongly impaired in their ability to oxidize chloride but still oxidized bromide, although they inactivate during turnover. The effects on the optical absorption spectrum of vanadium chloroperoxidase indicate that mutant H404A has a reduced affinity for the cofactor, whereas this affinity is unchanged in mutant D292A. The effect on the phosphatase activity of the apoenzyme was investigated for six mutants of putative catalytic residues. Effects of mutation of His-496, Arg-490, Arg-360, Lys-353, and His-404 to alanine are in line with their proposed roles in nucleophilic attack, transition-state stabilization, and leaving-group protonation. Asp-292 is excluded as the group that protonates the leaving group. A model based on the mutagenesis studies is presented and may serve as a template for glucose-6-phosphatase and other related phosphatases. Hydrolysis of a phospho-histidine intermediate is the rate-determining step in the phosphatase activity of apochloroperoxidase, as shown by burst kinetics.}, + pages = {11650--11657}, + number = {16}, + journaltitle = {Journal of Biological Chemistry}, + shortjournal = {Journal of Biological Chemistry}, + author = {Renirie, Rokus and Hemrika, Wieger and Wever, Ron}, + urldate = {2025-12-18}, + date = {2000-04-21}, + file = {PDF:/Users/davidtschan/Zotero/storage/LKIRYXFC/Renirie et al. - 2000 - Peroxidase and Phosphatase Activity of Active-site Mutants of Vanadium Chloroperoxidase from the Fun.pdf:application/pdf;ScienceDirect Snapshot:/Users/davidtschan/Zotero/storage/7YPEANDL/S0021925819808001.html:text/html}, +} + +@article{macedo-ribeiro_x-ray_1999, + title = {X-ray crystal structures of active site mutants of the vanadium-containing chloroperoxidase from the fungus Curvularia inaequalis}, + volume = {4}, + issn = {1432-1327}, + url = {https://doi.org/10.1007/s007750050306}, + doi = {10.1007/s007750050306}, + abstract = {The X-ray structures of the chloroperoxidase from Curvularia inaequalis, heterologously expressed in Saccharomyces cerevisiae, have been determined both in its apo and in its holo forms at 1.66 and 2.11 Å resolution, respectively. The crystal structures reveal that the overall structure of this enzyme remains nearly unaltered, particularly at the metal binding site. At the active site of the apo-chloroperoxidase structure a clearly defined sulfate ion was found, partially stabilised through electrostatic interactions and hydrogen bonds with positively charged residues involved in the interactions with the vanadate in the native protein. The vanadate binding pocket seems to form a very rigid frame stabilising oxyanion binding. The rigidity of this active site matrix is the result of a large number of hydrogen bonding interactions involving side chains and the main chain of residues lining the active site. The structures of single site mutants to alanine of the catalytic residue His404 and the vanadium protein ligand His496 have also been analysed. Additionally we determined the structural effects of mutations to alanine of residue Arg360, directly involved in the compensation of the negative charge of the vanadate group, and of residue Asp292 involved in forming a salt bridge with Arg490 which also interacts with the vanadate. The enzymatic chlorinating activity is drastically reduced to approximately 1\% in mutants D292A, H404A and H496A. The structures of the mutants confirm the view of the active site of this chloroperoxidase as a rigid matrix providing an oxyanion binding site. No large changes are observed at the active site for any of the analysed mutants. The empty space left by replacement of large side chains by alanines is usually occupied by a new solvent molecule which partially replaces the hydrogen bonding interactions to the vanadate. The new solvent molecules additionally replace part of the interactions the mutated side chains were making to other residues lining the active site frame. When this is not possible, another side chain in the proximity of the mutated residue moves in order to satisfy the hydrogen bonding potential of the residues located at the active site frame.}, + pages = {209--219}, + number = {2}, + journaltitle = {{JBIC} Journal of Biological Inorganic Chemistry}, + shortjournal = {{JBIC}}, + author = {Macedo-Ribeiro, Sandra and Hemrika, Wieger and Renirie, Rokus and Wever, Ron and Messerschmidt, A.}, + urldate = {2025-12-18}, + date = {1999-05-01}, + langid = {english}, + keywords = {Mutants, Phosphate, Chloroperoxidase, Key words Sulfate binding, Vanadate}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/6EPHGS65/Macedo-Ribeiro et al. - 1999 - X-ray crystal structures of active site mutants of the vanadium-containing chloroperoxidase from the.pdf:application/pdf}, +} + +@article{van_schijndel_chloroperoxidase_1993, + title = {The chloroperoxidase from the fungus \textit{Curvularia inaequalis}; a novel vanadium enzyme}, + volume = {1161}, + issn = {0167-4838}, + url = {https://www.sciencedirect.com/science/article/pii/016748389390221C}, + doi = {10.1016/0167-4838(93)90221-C}, + abstract = {The presence of vanadium-containing bromoperoxidases in various types of seaweed is well-documented. We now report that the terrestrial fungus Curvularia inaequalis excretes a novel chloroperoxidase which also contains vanadium as a prosthetic group. The chloroperoxidase is excreted in the medium as the only protein and is, therefore, almost purely obtained. Atomic absorption spectroscopy measurements showed that the chloroperoxidase contained vanadium, which was essential for enzymatic activity, in a stoichiometry of 1 mol vanadium per mol of enzyme. When the fungus was grown in media containing low concentrations of vanadate ({VO}43−) or when vanadate was absent, the enzyme was excreted in an apoform. Addition of vanadate to the apoenzyme purified from the medium, dialyzed holo-enzyme or growth medium led to incorporation of the metal and to a subsequent increase in specific activity from 0.7 to about 7.5 units/mg. The reduced enzyme showed an axially symmetric {EPR} spectrum (go = 1.971, Ao = 91.7 · 10−4cm−1) with 16 hyperfine lines that is essentially the same as the {EPR} spectrum of the vanadium-containing bromoperoxidase of the seaweed Ascophyllum nodosum. This demonstrates that the active sites in the two enzymes are very similar. The chlorinating and brominating activities of the chloroperoxidase from C. inaequalis were also studied and compared to those of the vanadium bromoperoxidase from A. nodosum. The chlorinating reaction catalyzed by the chloroperoxidase had a {pH} optimum around 5.5 and the Km for Cl− was small (0.25 {mM} at {pH} 4.5), but the logarithm of its value increased linearly with increasing {pH}. At high bromide concentrations, the {pH} optima of chloroperoxidase and bromoperoxidase in the brominating reaction were about the same (5.5). However, at low bromide concentrations the {pH} optimum of the chloroperoxidase was at higher {pH} values than that of the bromoperoxidase.}, + pages = {249--256}, + number = {2}, + journaltitle = {Biochimica et Biophysica Acta ({BBA}) - Protein Structure and Molecular Enzymology}, + shortjournal = {Biochimica et Biophysica Acta ({BBA}) - Protein Structure and Molecular Enzymology}, + author = {van Schijndel, Johannes W. P. M. and Vollenbroek, Esther G. M. and Wever, Ron}, + urldate = {2025-12-18}, + date = {1993-02-13}, + keywords = {Chloroperoxidase, (), Fungus, Vanadium}, + file = {PDF:/Users/davidtschan/Zotero/storage/LA4TPMPL/van Schijndel et al. - 1993 - The chloroperoxidase from the fungus Curvularia inaequalis\; a novel vanadium enzyme.pdf:application/pdf;ScienceDirect Snapshot:/Users/davidtschan/Zotero/storage/3NCH9FL6/016748389390221C.html:text/html}, +} + +@article{messerschmidt_implications_1997, + title = {Implications for the catalytic mechanism of the vanadium-containing enzyme chloroperoxidase from the fungus Curvularia inaequalis by X-ray structures of the native and peroxide form}, + volume = {378}, + issn = {1431-6730}, + doi = {10.1515/bchm.1997.378.3-4.309}, + abstract = {Implications for the catalytic mechanism of the vanadium-containing chloroperoxidase from the fungus Curvularia inaequalis have been obtained from the crystal structures of the native and peroxide forms of the enzyme. The X-ray structures have been solved by difference Fourier techniques using the atomic model of the azide chloroperoxidase complex. The 2.03 A crystal structure (R = 19.7\%) of the native enzyme reveals the geometry of the intact catalytic vanadium center. The vanadium is coordinated by four non-protein oxygen atoms and one nitrogen ({NE}2) atom from histidine 496 in a trigonal bipyramidal fashion. Three oxygens are in the equatorial plane and the fourth oxygen and the nitrogen are at the apexes of the bipyramid. In the 2.24 A crystal structure (R = 17.7\%) of the peroxide derivate the peroxide is bound to the vanadium in an eta2-fashion after the release of the apical oxygen ligand. The vanadium is coordinated also by 4 non-protein oxygen atoms and one nitrogen ({NE}2) from histidine 496. The coordination geometry around the vanadium is that of a distorted tetragonal pyramid with the two peroxide oxygens, one oxygen and the nitrogen in the basal plane and one oxygen in the apical position. A mechanism for the catalytic cycle has been proposed based on these X-ray structures and kinetic data.}, + pages = {309--315}, + number = {3}, + journaltitle = {Biological Chemistry}, + shortjournal = {Biol Chem}, + author = {Messerschmidt, A. and Prade, L. and Wever, R.}, + date = {1997}, + pmid = {9165086}, + keywords = {Binding Sites, Catalysis, Chloride Peroxidase, Crystallography, X-Ray, Fourier Analysis, Hydrogen Bonding, Mitosporic Fungi, Models, Molecular, Peroxides, Protein Conformation, Vanadium Compounds}, + file = {PDF:/Users/davidtschan/Zotero/storage/4GWB9BG7/Messerschmidt et al. - 1997 - Implications for the catalytic mechanism of the vanadium-containing enzyme chloroperoxidase from the.pdf:application/pdf}, +} + +@article{richter_production_2004, + title = {Production of methyl iodide in the tropical Atlantic Ocean}, + volume = {31}, + issn = {1944-8007}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1029/2004GL020779}, + doi = {10.1029/2004GL020779}, + abstract = {A series of 8 methyl iodide ({CH}3I) production experiments were conducted during Meteor cruise 55 to the tropical Atlantic. Natural seawater samples were incubated in quartz flasks, on-deck, for 24 hours both in the dark and under the natural light-dark cycle. A subset of incubations was conducted with samples that had been either filtered or poisoned to reduce or eliminate within-flask biological activity. The accumulation of {CH}3I in the dark incubations was {\textless}20\% of the ‘light’ production. The experimental results supported prior inferences that {CH}3I is produced in the open ocean by a light-dependent production pathway that is not directly dependent on biological activity. The average observed net production rate in full sunlight incubations was 2–5 nmol m−3 day−1. A mass balance for the tropical Atlantic surface layer implies that this rate of production can support at least 50\% of the average sea-to-air flux of 23 nmol m−2 day−1.}, + number = {23}, + journaltitle = {Geophysical Research Letters}, + author = {Richter, Uwe and Wallace, Douglas W. R.}, + urldate = {2025-12-19}, + date = {2004}, + langid = {english}, + note = {\_eprint: https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2004GL020779}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/JNDEDALV/Richter and Wallace - 2004 - Production of methyl iodide in the tropical Atlantic Ocean.pdf:application/pdf;Snapshot:/Users/davidtschan/Zotero/storage/KC48XVGI/2004GL020779.html:text/html}, +} + +@article{moore_photochemical_1994, + title = {Photochemical production of methyl iodide in seawater}, + volume = {99}, + rights = {http://onlinelibrary.wiley.com/{termsAndConditions}\#vor}, + issn = {0148-0227}, + url = {https://agupubs.onlinelibrary.wiley.com/doi/10.1029/94JD00786}, + doi = {10.1029/94JD00786}, + abstract = {It is generally acceptedthat methyl iodide is a major contributor to the flux of iodine from the ocean to the atmosphere, but its sourcesin the ocean are largely unknown, an exception being production by certain speciesof coastal macrophytic algae. Preliminary results reported here indicate production of methyl iodide in filtered seawater that has been irradiated with either sunlightor an artificial light source having a spectral output closely approximating to sunlightat sea level. The production was enhancedwhen the water sampleswere deoxygenatedand by the addition of iodide to this water. The results appear to be consistentwith a mechanisminvolving reaction between photochemicallyproduced methyl radicals and iodine atoms. It is estimated that the processis capable of making a significantcontribution to global iodine fluxes.}, + pages = {16415--16420}, + issue = {D8}, + journaltitle = {Journal of Geophysical Research: Atmospheres}, + shortjournal = {J. Geophys. Res.}, + author = {Moore, Robert M and Zafirious, Oliver C}, + urldate = {2025-12-19}, + date = {1994-08-20}, + langid = {english}, + file = {PDF:/Users/davidtschan/Zotero/storage/IT3AN7G7/1994 - Photochemical production of methyl iodide in seawater.pdf:application/pdf}, +} + +@article{odowd_marine_2002, + title = {Marine aerosol formation from biogenic iodine emissions}, + volume = {417}, + rights = {2002 Macmillan Magazines Ltd.}, + issn = {1476-4687}, + url = {https://www.nature.com/articles/nature00775}, + doi = {10.1038/nature00775}, + abstract = {The formation of marine aerosols and cloud condensation nuclei—from which marine clouds originate—depends ultimately on the availability of new, nanometre-scale particles in the marine boundary layer. Because marine aerosols and clouds scatter incoming radiation and contribute a cooling effect to the Earth's radiation budget1, new particle production is important in climate regulation. It has been suggested that sulphuric acid—derived from the oxidation of dimethyl sulphide—is responsible for the production of marine aerosols and cloud condensation nuclei. It was accordingly proposed that algae producing dimethyl sulphide play a role in climate regulation2, but this has been difficult to prove and, consequently, the processes controlling marine particle formation remains largely undetermined3,4. Here, using smog chamber experiments under coastal atmospheric conditions, we demonstrate that new particles can form from condensable iodine-containing vapours, which are the photolysis products of biogenic iodocarbons emitted from marine algae. Moreover, we illustrate, using aerosol formation models, that concentrations of condensable iodine-containing vapours over the open ocean are sufficient to influence marine particle formation. We suggest therefore that marine iodocarbon emissions have a potentially significant effect on global radiative forcing.}, + pages = {632--636}, + number = {6889}, + journaltitle = {Nature}, + author = {O'Dowd, Colin D. and Jimenez, Jose L. and Bahreini, Roya and Flagan, Richard C. and Seinfeld, John H. and Hämeri, Kaarle and Pirjola, Liisa and Kulmala, Markku and Jennings, S. Gerard and Hoffmann, Thorsten}, + urldate = {2025-12-19}, + date = {2002-06}, + langid = {english}, + note = {Publisher: Nature Publishing Group}, + keywords = {Humanities and Social Sciences, multidisciplinary, Science}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/8TFSBCI4/O'Dowd et al. - 2002 - Marine aerosol formation from biogenic iodine emissions.pdf:application/pdf}, +} + +@article{gilfedder_iodine_2008, + title = {Iodine speciation in rain, snow and aerosols}, + volume = {8}, + issn = {1680-7316}, + url = {https://acp.copernicus.org/articles/8/6069/2008/}, + doi = {10.5194/acp-8-6069-2008}, + abstract = {Iodine oxides, such as iodate, should be the only thermodynamically stable sink species for iodine in the troposphere. However, field observations have increasingly found very little iodate and significant amounts of iodide and soluble organically bound iodine ({SOI}) in precipitation and aerosols. The aim of this study was to investigate iodine speciation, including the organic fraction, in rain, snow, and aerosols in an attempt to further clarify aqueous phase iodine chemistry. Diurnal aerosol samples were taken with a 5 stage cascade impactor and a virtual impactor ({PM}2.5) from the Mace Head research station, Ireland, during summer 2006. Rain was collected from Australia, New Zealand, Patagonia, Germany, Ireland, and Switzerland and snow was obtained from Greenland, Germany, Switzerland, and New Zealand. Aerosols were extracted from the filters with water and all samples were analysed for total soluble iodine ({TSI}) by inductively coupled plasma mass spectrometry ({ICP}-{MS}) and iodine speciation was determined by coupling an ion chromatography unit to the {ICP}-{MS}. The median concentration of {TSI} in aerosols from Mace Head was 222 pmol m\−3 (summed over all impactor stages) of which the majority was associated with the {SOI} fraction (median day: 90\±4\%, night: 94\±2\% of total iodine). Iodide exhibited higher concentrations than iodate (median 6\% vs. 1.2\% of total iodine), and displayed significant enrichment during the day compared to the night. Interestingly, up to 5 additional, presumably anionic iodo-organic peaks were observed in all {IC}-{ICP}-{MS} chromatograms, composing up to 15\% of the {TSI}. Soluble organically bound iodine was also the dominant fraction in all rain and snow samples, with lesser amounts of iodide and iodate (iodate was particularly low in snow). Two of the same unidentified peaks found in aerosols were also observed in precipitation from both Southern and Northern Hemispheres. This suggests that these species are transferred from the aerosols into precipitation and that they have either a relatively long lifetime or are rapidly recycled. It is thought that {SOI} is formed by reactions between {HOI} or I2 and organic matter derived from the ocean surface layer. {SOI} may then photolytically decompose to yield iodide and the unidentified species. The data in this study show that iodine oxides are the least abundant species in rain, snow, and aerosols and therefore considerably more effort is required on aqueous phase iodine chemistry for a holistic understanding of the iodine cycle.}, + pages = {6069--6084}, + number = {20}, + journaltitle = {Atmospheric Chemistry and Physics}, + author = {Gilfedder, B. S. and Lai, S. C. and Petri, M. and Biester, H. and Hoffmann, T.}, + urldate = {2025-12-19}, + date = {2008-10-21}, + note = {Publisher: Copernicus {GmbH}}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/B9WCYLXU/Gilfedder et al. - 2008 - Iodine speciation in rain, snow and aerosols.pdf:application/pdf}, +} + +@article{cuevas_rapid_2018, + title = {Rapid increase in atmospheric iodine levels in the North Atlantic since the mid-20th century}, + volume = {9}, + rights = {2018 The Author(s)}, + issn = {2041-1723}, + url = {https://www.nature.com/articles/s41467-018-03756-1}, + doi = {10.1038/s41467-018-03756-1}, + abstract = {Atmospheric iodine causes tropospheric ozone depletion and aerosol formation, both of which have significant climate impacts, and is an essential dietary element for humans. However, the evolution of atmospheric iodine levels at decadal and centennial scales is unknown. Here, we report iodine concentrations in the {RECAP} ice-core (coastal East Greenland) to investigate how atmospheric iodine levels in the North Atlantic have evolved over the past 260 years (1750–2011), this being the longest record of atmospheric iodine in the Northern Hemisphere. The levels of iodine tripled from 1950 to 2010. Our results suggest that this increase is driven by anthropogenic ozone pollution and enhanced sub-ice phytoplankton production associated with the recent thinning of Arctic sea ice. Increasing atmospheric iodine has accelerated ozone loss and has considerably enhanced iodine transport and deposition to the Northern Hemisphere continents. Future climate and anthropogenic forcing may continue to amplify oceanic iodine emissions with potentially significant health and environmental impacts at global scale.}, + pages = {1452}, + number = {1}, + journaltitle = {Nature Communications}, + shortjournal = {Nat Commun}, + author = {Cuevas, Carlos A. and Maffezzoli, Niccolò and Corella, Juan Pablo and Spolaor, Andrea and Vallelonga, Paul and Kjær, Helle A. and Simonsen, Marius and Winstrup, Mai and Vinther, Bo and Horvat, Christopher and Fernandez, Rafael P. and Kinnison, Douglas and Lamarque, Jean-François and Barbante, Carlo and Saiz-Lopez, Alfonso}, + urldate = {2025-12-20}, + date = {2018-04-13}, + langid = {english}, + note = {Publisher: Nature Publishing Group}, + keywords = {Atmospheric chemistry}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/RAYIHXSB/Cuevas et al. - 2018 - Rapid increase in atmospheric iodine levels in the North Atlantic since the mid-20th century.pdf:application/pdf}, +} + +@article{he_role_2021, + title = {Role of iodine oxoacids in atmospheric aerosol nucleation}, + volume = {371}, + url = {https://www.science.org/doi/full/10.1126/science.abe0298}, + doi = {10.1126/science.abe0298}, + abstract = {Iodic acid ({HIO}3) is known to form aerosol particles in coastal marine regions, but predicted nucleation and growth rates are lacking. Using the {CERN} {CLOUD} (Cosmics Leaving Outdoor Droplets) chamber, we find that the nucleation rates of {HIO}3 particles are rapid, even exceeding sulfuric acid–ammonia rates under similar conditions. We also find that ion-induced nucleation involves {IO}3− and the sequential addition of {HIO}3 and that it proceeds at the kinetic limit below +10°C. In contrast, neutral nucleation involves the repeated sequential addition of iodous acid ({HIO}2) followed by {HIO}3, showing that {HIO}2 plays a key stabilizing role. Freshly formed particles are composed almost entirely of {HIO}3, which drives rapid particle growth at the kinetic limit. Our measurements indicate that iodine oxoacid particle formation can compete with sulfuric acid in pristine regions of the atmosphere.}, + pages = {589--595}, + number = {6529}, + journaltitle = {Science}, + author = {He, Xu-Cheng and Tham, Yee Jun and Dada, Lubna and Wang, Mingyi and Finkenzeller, Henning and Stolzenburg, Dominik and Iyer, Siddharth and Simon, Mario and Kürten, Andreas and Shen, Jiali and Rörup, Birte and Rissanen, Matti and Schobesberger, Siegfried and Baalbaki, Rima and Wang, Dongyu S. and Koenig, Theodore K. and Jokinen, Tuija and Sarnela, Nina and Beck, Lisa J. and Almeida, João and Amanatidis, Stavros and Amorim, António and Ataei, Farnoush and Baccarini, Andrea and Bertozzi, Barbara and Bianchi, Federico and Brilke, Sophia and Caudillo, Lucía and Chen, Dexian and Chiu, Randall and Chu, Biwu and Dias, António and Ding, Aijun and Dommen, Josef and Duplissy, Jonathan and El Haddad, Imad and Gonzalez Carracedo, Loïc and Granzin, Manuel and Hansel, Armin and Heinritzi, Martin and Hofbauer, Victoria and Junninen, Heikki and Kangasluoma, Juha and Kemppainen, Deniz and Kim, Changhyuk and Kong, Weimeng and Krechmer, Jordan E. and Kvashin, Aleksander and Laitinen, Totti and Lamkaddam, Houssni and Lee, Chuan Ping and Lehtipalo, Katrianne and Leiminger, Markus and Li, Zijun and Makhmutov, Vladimir and Manninen, Hanna E. and Marie, Guillaume and Marten, Ruby and Mathot, Serge and Mauldin, Roy L. and Mentler, Bernhard and Möhler, Ottmar and Müller, Tatjana and Nie, Wei and Onnela, Antti and Petäjä, Tuukka and Pfeifer, Joschka and Philippov, Maxim and Ranjithkumar, Ananth and Saiz-Lopez, Alfonso and Salma, Imre and Scholz, Wiebke and Schuchmann, Simone and Schulze, Benjamin and Steiner, Gerhard and Stozhkov, Yuri and Tauber, Christian and Tomé, António and Thakur, Roseline C. and Väisänen, Olli and Vazquez-Pufleau, Miguel and Wagner, Andrea C. and Wang, Yonghong and Weber, Stefan K. and Winkler, Paul M. and Wu, Yusheng and Xiao, Mao and Yan, Chao and Ye, Qing and Ylisirniö, Arttu and Zauner-Wieczorek, Marcel and Zha, Qiaozhi and Zhou, Putian and Flagan, Richard C. and Curtius, Joachim and Baltensperger, Urs and Kulmala, Markku and Kerminen, Veli-Matti and Kurtén, Theo and Donahue, Neil M. and Volkamer, Rainer and Kirkby, Jasper and Worsnop, Douglas R. and Sipilä, Mikko}, + urldate = {2025-12-20}, + date = {2021-02-05}, + note = {Publisher: American Association for the Advancement of Science}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/D7Z3SXVJ/He et al. - 2021 - Role of iodine oxoacids in atmospheric aerosol nucleation.pdf:application/pdf}, +} + +@article{luther_review_2023, + title = {Review on the physical chemistry of iodine transformations in the oceans}, + volume = {10}, + issn = {2296-7745}, + url = {https://www.frontiersin.org/journals/marine-science/articles/10.3389/fmars.2023.1085618/full}, + doi = {10.3389/fmars.2023.1085618}, + abstract = {The transformation between iodate ({IO}3-), the thermodynamically stable form of iodine, and iodide (I-), the kinetically stable form of iodine, has received much attention because these species are often dependent on the oxygen concentration, which ranges from saturation to non-detectable in the ocean. As suboxic conditions in the ocean’s major oxygen minimum zones indicate that {IO}3- is minimal or non-detectable, the incorporation of {IO}3- into carbonate minerals has been used as a redox proxy to determine the O2 state of the ocean. Here, I look at the one and two electron transfers between iodine species with a variety of oxidants and reductants to show thermodynamics of these transformations. The {IO}3- to {IO}2- conversion is shown to be the controlling step in the reduction reaction sequence due to thermodynamic considerations. As {IO}3- reduction to {IO}2- is more favorable than {NO}3- reduction to {NO}2- at oceanic {pH} values, there is no need for nitrate reductase for {IO}3- reduction as other reductants (e.g. Fe2+, Mn2+) and dissimilatory {IO}3– reduction by microbes during organic matter decomposition can affect the transformation. Unfortunately, there is a dearth of information on the kinetics of reductants with {IO}3-; thus, the thermodynamic calculations suggest avenues for research. Conversely, there is significant information on the kinetics of I- oxidation with various oxygen species. In the environment, I- oxidation is the controlling step for oxidation. The oxidants that can lead to {IO}3- are reactive oxygen species with O3 and •{OH} being the most potent as well as sedimentary oxidized Mn, which occurs at lower {pH} than ocean waters. Recent work has shown that iodide oxidizing bacteria can also form {IO}3-. I- oxidation is more facile at the sea surface microlayer and in the atmosphere due to O3.}, + journaltitle = {Frontiers in Marine Science}, + shortjournal = {Front. Mar. Sci.}, + author = {Luther, George W.}, + urldate = {2025-12-20}, + date = {2023-02-15}, + note = {Publisher: Frontiers}, + keywords = {Iodate, Iodide, iodine intermediates, Oxidation, Reduction, Thermodynamics}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/JYJTWFIM/Luther - 2023 - Review on the physical chemistry of iodine transformations in the oceans.pdf:application/pdf}, +} + +@article{truesdale_circumstantial_2012, + title = {Circumstantial evidence in support of org-I as a component of the marine aerosol arising from a study of marine foams}, + volume = {115}, + issn = {02727714}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S027277141200306X}, + doi = {10.1016/j.ecss.2012.08.003}, + abstract = {A study of foams formed on the marine Lake Mir, Croatia, and elsewhere on the same coast demonstrates, for the first time, that they are fractionated (enrichened) in org-I by up to 630 times relative to the water from which they form. The results are consistent with an I/C mole ratio for in-situ organic matter. Foams created artificially in the laboratory from natural samples of water from Lake Mir were similarly fractionated, although to a lesser degree. These differences were effectively removed when enrichments were expressed as molar ratios, e.g., Ptot/Itot, rather than straightforward concentrations. This similarity in the behaviour to enrichment for organic forms of I, N and P suggests that the time over which foams age is a major determinant of the enrichment they display. It is argued that this period allows time for the seawater occluded in the interstitial spaces between bubbles, to drain away. Since foam production is ubiquitous over the oceans it seems likely that this process local to coastal environments is much more common than at first might appear to be the case. The paper explains how this work provides circumstantial evidence that the bubble-bursting mechanism current since the 1960s may well provide the iodine which appears to be missing in many modelling calculations based upon an atmospheric system dependant upon sorption of the species {IO} upon the marine aerosol.}, + pages = {388--398}, + journaltitle = {Estuarine, Coastal and Shelf Science}, + shortjournal = {Estuarine, Coastal and Shelf Science}, + author = {Truesdale, Victor W. and Žic, Vesna and Garnier, Cédric and Cukrov, Neven}, + urldate = {2025-12-20}, + date = {2012-12}, + langid = {english}, + file = {PDF:/Users/davidtschan/Zotero/storage/XU8YSRL7/Truesdale et al. - 2012 - Circumstantial evidence in support of org-I as a component of the marine aerosol arising from a stud.pdf:application/pdf}, +} + +@article{elderfield_biophilic_1980, + title = {On the biophilic nature of iodine in seawater}, + volume = {50}, + issn = {0012-821X}, + url = {https://www.sciencedirect.com/science/article/pii/0012821X80901223}, + doi = {10.1016/0012-821X(80)90122-3}, + abstract = {Vertical profiles of concentrations of iodate- and total-iodine have been measured at thirty stations in the Pacific, Atlantic and Antarctic Oceans. The salinity-normalised iodine profiles are indicative of both iodine removal and iodate reduction in the euphotic zone. Thus, surface waters appear to be depleted in iodate-iodine (by 0.03−0.22 μM) but less so in total-iodine (by{\textless}0.01−0.06 μM) when compared with the near-constant iodine concentrations (∼0.46 μM) at depth. Graphs of specific total-iodine versus specific phosphate fit a linear model well and lie within a narrow envelope for all stations, suggesting a direct coupling of iodine and nutrients during assimilation/regeneration. The I/C atom ratio calculated from these hydrographic data (1.0 × 10−4) agrees well with contemporary plankton compositions (I/C= 1.4 (±0.8) × 10−4). Similar graphs involving specific iodate also fit a linear model well. However, their gradients vary from station to station leading to a variability in I/C interconversion ratio, analogous to the variability of Redfield nutrient ratios for coastal waters. This variation is attributed to changes in both productivity and nitrate availability. Pacific deep waters contain anomalously high total-iodine concentrations which may reflect regional differences of I/P ratio in surface waters or else diffusion of iodine from bottom sediments.}, + pages = {105--114}, + number = {1}, + journaltitle = {Earth and Planetary Science Letters}, + shortjournal = {Earth and Planetary Science Letters}, + author = {Elderfield, Henry and Truesdale, Victor W.}, + urldate = {2025-12-20}, + date = {1980-10-01}, + file = {PDF:/Users/davidtschan/Zotero/storage/8JRTTMLZ/Elderfield and Truesdale - 1980 - On the biophilic nature of iodine in seawater.pdf:application/pdf;ScienceDirect Snapshot:/Users/davidtschan/Zotero/storage/Z655HX28/0012821X80901223.html:text/html}, +} + +@article{carpenter_atmospheric_2013, + title = {Atmospheric iodine levels influenced by sea surface emissions of inorganic iodine}, + volume = {6}, + rights = {2013 Springer Nature Limited}, + issn = {1752-0908}, + url = {https://www.nature.com/articles/ngeo1687}, + doi = {10.1038/ngeo1687}, + abstract = {Naturally occurring bromine- and iodine-containing compounds substantially reduce regional, and possibly global, tropospheric ozone levels. Experimental and model results suggest that the reaction of ozone with iodide could account for around 75\% of observed iodine oxide levels over the tropical Atlantic Ocean.}, + pages = {108--111}, + number = {2}, + journaltitle = {Nature Geoscience}, + shortjournal = {Nature Geosci}, + author = {Carpenter, Lucy J. and {MacDonald}, Samantha M. and Shaw, Marvin D. and Kumar, Ravi and Saunders, Russell W. and Parthipan, Rajendran and Wilson, Julie and Plane, John M. C.}, + urldate = {2025-12-20}, + date = {2013-02}, + langid = {english}, + note = {Publisher: Nature Publishing Group}, + keywords = {Atmospheric chemistry, Biogeochemistry}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/FLGJMTLQ/Carpenter et al. - 2013 - Atmospheric iodine levels influenced by sea surface emissions of inorganic iodine.pdf:application/pdf}, +} + +@article{sherwen_global_2016, + title = {Global modeling of tropospheric iodine aerosol}, + volume = {43}, + rights = {©2016. The Authors.}, + issn = {1944-8007}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/2016GL070062}, + doi = {10.1002/2016GL070062}, + abstract = {Natural aerosols play a central role in the Earth system. The conversion of dimethyl sulfide to sulfuric acid is the dominant source of oceanic secondary aerosol. Ocean emitted iodine can also produce aerosol. Using a {GEOS}-Chem model, we present a simulation of iodine aerosol. The simulation compares well with the limited observational data set. Iodine aerosol concentrations are highest in the tropical marine boundary layer ({MBL}) averaging 5.2 ng (I) m−3 with monthly maximum concentrations of 90 ng (I) m−3. These masses are small compared to sulfate (0.75\% of {MBL} burden, up to 11\% regionally) but are more significant compared to dimethyl sulfide sourced sulfate (3\% of the {MBL} burden, up to 101\% regionally). In the preindustrial, iodine aerosol makes up 0.88\% of the {MBL} burden sulfate mass and regionally up to 21\%. Iodine aerosol may be an important regional mechanism for ocean-atmosphere interaction.}, + pages = {10012--10019}, + number = {18}, + journaltitle = {Geophysical Research Letters}, + author = {Sherwen, Tomás M. and Evans, Mat J. and Spracklen, Dominick V. and Carpenter, Lucy J. and Chance, Rosie and Baker, Alex R. and Schmidt, Johan A. and Breider, Thomas J.}, + urldate = {2025-12-20}, + date = {2016}, + langid = {english}, + note = {\_eprint: https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1002/2016GL070062}, + keywords = {aerosol, dimethyl sulfide, {DMS}, iodine, marine boundary layer, sulfate}, + file = {Full Text:/Users/davidtschan/Zotero/storage/Q3UJU7IR/Sherwen et al. - 2016 - Global modeling of tropospheric iodine aerosol.pdf:application/pdf;Snapshot:/Users/davidtschan/Zotero/storage/FVLAGP3X/2016GL070062.html:text/html}, +} + +@article{saiz-lopez_injection_2015, + title = {Injection of iodine to the stratosphere}, + volume = {42}, + rights = {©2015. American Geophysical Union. All Rights Reserved.}, + issn = {1944-8007}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/2015GL064796}, + doi = {10.1002/2015GL064796}, + abstract = {We report a new estimation of the injection of iodine into the stratosphere based on novel daytime (solar zenith angle {\textless} 45°) aircraft observations in the tropical tropopause layer and a global atmospheric model with the most recent knowledge about iodine photochemistry. The results indicate that significant levels of total reactive iodine (0.25–0.7 parts per trillion by volume), between 2 and 5 times larger than the accepted upper limits, can be injected into the stratosphere via tropical convective outflow. At these iodine levels, modeled iodine catalytic cycles account for up to 30\% of the contemporary ozone loss in the tropical lower stratosphere and can exert a stratospheric ozone depletion potential equivalent to, or even larger than, that of very short-lived bromocarbons. Therefore, we suggest that iodine sources and chemistry need to be considered in assessments of the historical and future evolution of the stratospheric ozone layer.}, + pages = {6852--6859}, + number = {16}, + journaltitle = {Geophysical Research Letters}, + author = {Saiz-Lopez, A. and Baidar, S. and Cuevas, C. A. and Koenig, T. K. and Fernandez, R. P. and Dix, B. and Kinnison, D. E. and Lamarque, J.-F. and Rodriguez-Lloveras, X. and Campos, T. L. and Volkamer, R.}, + urldate = {2025-12-20}, + date = {2015}, + langid = {english}, + note = {\_eprint: https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1002/2015GL064796}, + keywords = {iodine, ozone, stratosphere}, + file = {PDF:/Users/davidtschan/Zotero/storage/4IWIUJD2/Saiz-Lopez et al. - 2015 - Injection of iodine to the stratosphere.pdf:application/pdf;Snapshot:/Users/davidtschan/Zotero/storage/MJWNUBHL/2015GL064796.html:text/html}, +} + +@article{koenig_ozone_2021, + title = {Ozone depletion due to dust release of iodine in the free troposphere}, + volume = {7}, + url = {https://www.science.org/doi/full/10.1126/sciadv.abj6544}, + doi = {10.1126/sciadv.abj6544}, + abstract = {Iodine is an atmospheric trace element emitted from oceans that efficiently destroys ozone (O3). Low O3 in airborne dust layers is frequently observed but poorly understood. We show that dust is a source of gas-phase iodine, indicated by aircraft observations of iodine monoxide ({IO}) radicals inside lofted dust layers from the Atacama and Sechura Deserts that are up to a factor of 10 enhanced over background. Gas-phase iodine photochemistry, commensurate with observed {IO}, is needed to explain the low O3 inside these dust layers (below 15 ppbv; up to 75\% depleted). The added dust iodine can explain decreases in O3 of 8\% regionally and affects surface air quality. Our data suggest that iodate reduction to form volatile iodine species is a missing process in the geochemical iodine cycle and presents an unrecognized aeolian source of iodine. Atmospheric iodine has tripled since 1950 and affects ozone layer recovery and particle formation.}, + pages = {eabj6544}, + number = {52}, + journaltitle = {Science Advances}, + author = {Koenig, Theodore K. and Volkamer, Rainer and Apel, Eric C. and Bresch, James F. and Cuevas, Carlos A. and Dix, Barbara and Eloranta, Edwin W. and Fernandez, Rafael P. and Hall, Samuel R. and Hornbrook, Rebecca S. and Pierce, R. Bradley and Reeves, J. Michael and Saiz-Lopez, Alfonso and Ullmann, Kirk}, + urldate = {2025-12-20}, + date = {2021-12-22}, + note = {Publisher: American Association for the Advancement of Science}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/BL8CCXZJ/Koenig et al. - 2021 - Ozone depletion due to dust release of iodine in the free troposphere.pdf:application/pdf}, +} + +@article{mahajan_measurement_2010, + title = {Measurement and modelling of tropospheric reactive halogen species over the tropical Atlantic Ocean}, + volume = {10}, + issn = {1680-7316}, + url = {https://acp.copernicus.org/articles/10/4611/2010/}, + doi = {10.5194/acp-10-4611-2010}, + abstract = {Although tropospheric reactive halogen chemistry is well studied in coastal and polar environments, the presence of halogens over the open ocean environment has not been widely reported. The impacts of halogens on the tropical open ocean marine boundary layer ({MBL}), in particular, are not well characterised. This paper describes observations of iodine monoxide ({IO}) and bromine oxide ({BrO}) over eight months in the tropical open ocean {MBL}, on the north-eastern side of São Vicente (Cape Verde Islands, 16.85° N, 24.87° W). The highest {BrO} mixing ratio observed was 5.6\±1 pmol mol−1, while the maximum observed {IO} mixing ratio was 3.1±0.4 pmol mol−1. The average values seen between 09:00–17:00 {GMT} were {\textasciitilde}2.8 pmol mol−1 for {BrO} and {\textasciitilde}1.5 pmol mol−1 for {IO}; these averages showed little variability over the entire campaign from November 2006 to June 2007. A 1-dimensional chemistry and transport model is used to study the evolution of iodine species and quantify the combined impact of iodine and bromine chemistry on the oxidising capacity of the {MBL}. It appears that the measured fluxes of iodocarbons are insufficient to account for the observed levels of {IO}, and that an additional I atom source is required, possibly caused by the deposition of O3 onto the ocean surface in the presence of solar radiation. Modelling results also show that the O3 depletion observed at Cape Verde cannot be explained in the absence of halogen chemistry, which contributes {\textasciitilde}45\% of the observed O3 depletion at the height of measurements (10 m) during summer. The model also predicts that halogens decrease the hydroperoxy radical ({HO}2) concentration by {\textasciitilde}14\% and increase the hydroxyl radical ({OH}) concentration by {\textasciitilde}13\% near the ocean surface. The oxidation of dimethyl sulphide ({DMS}) by {BrO} takes place at a comparable rate to oxidation by {OH} in this environment. Finally, the potential of iodine chemistry to form new particles is explored and conditions under which particle formation could be important in the remote {MBL} are discussed.}, + pages = {4611--4624}, + number = {10}, + journaltitle = {Atmospheric Chemistry and Physics}, + author = {Mahajan, A. S. and Plane, J. M. C. and Oetjen, H. and Mendes, L. and Saunders, R. W. and Saiz-Lopez, A. and Jones, C. E. and Carpenter, L. J. and {McFiggans}, G. B.}, + urldate = {2025-12-20}, + date = {2010-05-19}, + note = {Publisher: Copernicus {GmbH}}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/WPW34K7K/Mahajan et al. - 2010 - Measurement and modelling of tropospheric reactive halogen species over the tropical Atlantic Ocean.pdf:application/pdf}, +} + +@article{pillar-little_conversion_2013, + title = {Conversion of Iodide to Hypoiodous Acid and Iodine in Aqueous Microdroplets Exposed to Ozone}, + volume = {47}, + issn = {0013-936X}, + url = {https://doi.org/10.1021/es401700h}, + doi = {10.1021/es401700h}, + abstract = {Halides are incorporated into aerosol sea spray, where they start the catalytic destruction of ozone (O3) over the oceans and affect the global troposphere. Two intriguing environmental problems undergoing continuous research are (1) to understand how reactive gas phase molecular halogens are directly produced from inorganic halides exposed to O3 and (2) to constrain the environmental factors that control this interfacial process. This paper presents a laboratory study of the reaction of O3 at variable iodide (I–) concentration (0.010–100 μM) for solutions aerosolized at 25 °C, which reveal remarkable differences in the reaction intermediates and products expected in sea spray for low tropospheric [O3]. The ultrafast oxidation of I– by O3 at the air–water interface of microdroplets is evidenced by the appearance of hypoiodous acid ({HIO}), iodite ({IO}2–), iodate ({IO}3–), triiodide (I3–), and molecular iodine (I2). Mass spectrometry measurements reveal an enhancement (up to 28\%) in the dissolution of gaseous O3 at the gas–liquid interface when increasing the concentration of {NaI} or {NaBr} from 0.010 to 100 μM. The production of iodine species such as {HIO} and I2 from {NaI} aerosolized solutions exposed to 50 ppbv O3 can occur at the air–water interface of sea spray, followed by their transfer to the gas-phase, where they contribute to the loss of tropospheric ozone.}, + pages = {10971--10979}, + number = {19}, + journaltitle = {Environmental Science \& Technology}, + shortjournal = {Environ. Sci. Technol.}, + author = {Pillar-Little, Elizabeth A. and Guzman, Marcelo I. and Rodriguez, Jose M.}, + urldate = {2025-12-20}, + date = {2013-10-01}, + note = {Publisher: American Chemical Society}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/9RVZL4ES/Pillar-Little et al. - 2013 - Conversion of Iodide to Hypoiodous Acid and Iodine in Aqueous Microdroplets Exposed to Ozone.pdf:application/pdf}, +} + +@article{bloss_kinetics_2001, + title = {Kinetics and Products of the {IO} Self-Reaction}, + volume = {105}, + issn = {1089-5639}, + url = {https://doi.org/10.1021/jp0044936}, + doi = {10.1021/jp0044936}, + abstract = {The absorption cross sections of the gas-phase {IO} radical and the kinetics and products of the {IO} self-reaction have been measured using the technique of laser photolysis with time-resolved {UV}−vis absorption spectroscopy. The {IO} absorption cross section at the peak of the (4,0) vibronic band of the (A2Π ← X 2Π) transition at 427.2 nm, determined using the reaction O(3P) + {CF}3I to form {IO} and calibrated relative to the O3 cross section was found to be (1.9 ± 0.17) × 10-17 cm2molecule-1 at 295 K and 1.13 nm fwhm spectral resolution. The {IO} cross sections were found to exhibit a negative temperature dependence. The kinetics of the {IO} self-reaction were measured using the reaction O(3P) + I2 to form {IO}, and the self-reaction rate coefficient k1, determined from the loss of {IO} radicals in the absence of ozone, was found to be (8.2 ± 1.3) × 10-11 molecules-1 cm3 s-1 at 295 K and 760 Torr. The self-reaction rate coefficient was found to be independent of pressure between 100 and 760 Torr, and to display a negative temperature dependence between 222 and 325 K, described by k1 = (4.1 ± 3.4) × 10-11 exp\{(220 ± 230)/T\} molecules-1 cm3 s-1. All errors are 2σ. Four potential product channels exist for the {IO} self-reaction:  {IO} + {IO} → 2I + O2 (1a), {IO} + {IO} → I2 + O2 (1b), {IO} + {IO} → {OIO} + I (1c), {IO} + {IO} + M → I2O2 + M (1d). No direct measurement of I atom production was performed. I2 formation was observed, but attributed to {IO}-catalyzed I atom recombination (I + {IO} + M → I2O + M; I + I2O → I2 + {IO}). {OIO} formation was observed and shown to result from the {IO} self-reaction. Formation of a broadband absorbing product underlying the {IO} absorption at low (λ {\textless} 400 nm) wavelengths was observed, and tentatively attributed to I2O2. The {OIO} cross sections and yield from the {IO} + {IO} reaction were determined via measurement of {OIO} production from the {IO} + {BrO} reaction which allowed limits to be placed on the branching ratio for {OIO} formation in the {IO} self-reaction at 295 K and 760 Torr. Branching ratios for all reaction channels were found to lie in the ranges 0.07 ≤ k1a/k1 ≤ 0.15, k1b/k1 ≤ 0.05, 0.30 ≤ k1c/k1 ≤ 0.46, and 0.42 ≤ k1d/k1 ≤ 0.55 at 295 K and 760 Torr. The results are compared with previous studies of the {IO} self-reaction, and their implications for atmospheric iodine chemistry are considered.}, + pages = {7840--7854}, + number = {33}, + journaltitle = {The Journal of Physical Chemistry A}, + shortjournal = {J. Phys. Chem. A}, + author = {Bloss, William J. and Rowley, David M. and Cox, R. Anthony and Jones, Roderic L.}, + urldate = {2025-12-21}, + date = {2001-08-01}, + note = {Publisher: American Chemical Society}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/I3QAU5ZR/Bloss et al. - 2001 - Kinetics and Products of the IO Self-Reaction.pdf:application/pdf}, +} + +@article{dix_detection_2013, + title = {Detection of iodine monoxide in the tropical free troposphere}, + volume = {110}, + url = {https://www.pnas.org/doi/abs/10.1073/pnas.1212386110}, + doi = {10.1073/pnas.1212386110}, + abstract = {Atmospheric iodine monoxide ({IO}) is a radical that catalytically destroys heat trapping +ozone and reacts further to form aerosols. Here, we report ...}, + pages = {2035--2040}, + number = {6}, + journaltitle = {Proceedings of the National Academy of Sciences}, + author = {Dix, Barbara and Baidar, Sunil and Bresch, James F. and Hall, Samuel R. and Schmidt, K. Sebastian and Wang, Siyuan and Volkamer, Rainer}, + urldate = {2025-12-21}, + date = {2013-02-05}, + note = {Company: National Academy of Sciences +Distributor: National Academy of Sciences +Institution: National Academy of Sciences +Label: National Academy of Sciences +Publisher: Proceedings of the National Academy of Sciences}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/DYIJVE5I/Dix et al. - 2013 - Detection of iodine monoxide in the tropical free troposphere.pdf:application/pdf}, +} + +@article{finkenzeller_gas-phase_2023, + title = {The gas-phase formation mechanism of iodic acid as an atmospheric aerosol source}, + volume = {15}, + rights = {2022 The Author(s)}, + issn = {1755-4349}, + url = {https://www.nature.com/articles/s41557-022-01067-z}, + doi = {10.1038/s41557-022-01067-z}, + abstract = {Iodine is a reactive trace element in atmospheric chemistry that destroys ozone and nucleates particles. Iodine emissions have tripled since 1950 and are projected to keep increasing with rising O3 surface concentrations. Although iodic acid ({HIO}3) is widespread and forms particles more efficiently than sulfuric acid, its gas-phase formation mechanism remains unresolved. Here, in {CLOUD} atmospheric simulation chamber experiments that generate iodine radicals at atmospherically relevant rates, we show that iodooxy hypoiodite, {IOIO}, is efficiently converted into {HIO}3 via reactions (R1) {IOIO} + O3 → {IOIO}4 and (R2) {IOIO}4 + H2O → {HIO}3 + {HOI} + (1)O2. The laboratory-derived reaction rate coefficients are corroborated by theory and shown to explain field observations of daytime {HIO}3 in the remote lower free troposphere. The mechanism provides a missing link between iodine sources and particle formation. Because particulate iodate is readily reduced, recycling iodine back into the gas phase, our results suggest a catalytic role of iodine in aerosol formation.}, + pages = {129--135}, + number = {1}, + journaltitle = {Nature Chemistry}, + shortjournal = {Nat. Chem.}, + author = {Finkenzeller, Henning and Iyer, Siddharth and He, Xu-Cheng and Simon, Mario and Koenig, Theodore K. and Lee, Christopher F. and Valiev, Rashid and Hofbauer, Victoria and Amorim, Antonio and Baalbaki, Rima and Baccarini, Andrea and Beck, Lisa and Bell, David M. and Caudillo, Lucía and Chen, Dexian and Chiu, Randall and Chu, Biwu and Dada, Lubna and Duplissy, Jonathan and Heinritzi, Martin and Kemppainen, Deniz and Kim, Changhyuk and Krechmer, Jordan and Kürten, Andreas and Kvashnin, Alexandr and Lamkaddam, Houssni and Lee, Chuan Ping and Lehtipalo, Katrianne and Li, Zijun and Makhmutov, Vladimir and Manninen, Hanna E. and Marie, Guillaume and Marten, Ruby and Mauldin, Roy L. and Mentler, Bernhard and Müller, Tatjana and Petäjä, Tuukka and Philippov, Maxim and Ranjithkumar, Ananth and Rörup, Birte and Shen, Jiali and Stolzenburg, Dominik and Tauber, Christian and Tham, Yee Jun and Tomé, António and Vazquez-Pufleau, Miguel and Wagner, Andrea C. and Wang, Dongyu S. and Wang, Mingyi and Wang, Yonghong and Weber, Stefan K. and Nie, Wei and Wu, Yusheng and Xiao, Mao and Ye, Qing and Zauner-Wieczorek, Marcel and Hansel, Armin and Baltensperger, Urs and Brioude, Jérome and Curtius, Joachim and Donahue, Neil M. and Haddad, Imad El and Flagan, Richard C. and Kulmala, Markku and Kirkby, Jasper and Sipilä, Mikko and Worsnop, Douglas R. and Kurten, Theo and Rissanen, Matti and Volkamer, Rainer}, + urldate = {2025-12-21}, + date = {2023-01}, + langid = {english}, + note = {Publisher: Nature Publishing Group}, + keywords = {Atmospheric chemistry, Photochemistry, Physical chemistry}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/2E69UCZS/Finkenzeller et al. - 2023 - The gas-phase formation mechanism of iodic acid as an atmospheric aerosol source.pdf:application/pdf}, +} + +@article{oldridge_formation_2011, + title = {Formation of Gas-Phase Bromine from Interaction of Ozone with Frozen and Liquid {NaCl}/{NaBr} Solutions: Quantitative Separation of Surficial Chemistry from Bulk-Phase Reaction}, + volume = {115}, + issn = {1089-5639}, + url = {https://doi.org/10.1021/jp200074u}, + doi = {10.1021/jp200074u}, + shorttitle = {Formation of Gas-Phase Bromine from Interaction of Ozone with Frozen and Liquid {NaCl}/{NaBr} Solutions}, + abstract = {The formation kinetics of gas-phase bromine (Br2) from interaction of gas-phase ozone (O3) with frozen and liquid solutions of {NaCl} (0.55 M) and {NaBr} (largely from 1.7 to 8.5 {mM}) have been studied from −40 to 0 °C in a coated-wall flow tube coupled to a chemical ionization mass spectrometer. The reactive uptake coefficient for O3 is deduced from the product formation rate and then studied as a function of experimental conditions. In particular, for both the liquid and frozen solutions, we find that the uptake coefficient is inversely dependent on the gas-phase O3 concentration in a manner that is quantitatively consistent with both surface- and bulk-phase kinetics. The reaction is fastest on acidic media ({pH} of the starting solution down to 2) but also proceeds at an appreciable rate on neutral substrates. Above 253 K, the uptake coefficient increases with increasing temperature on frozen solutions, consistent with an increasing brine content. The similarity of the absolute magnitude and form of the kinetics on the frozen and liquid substrates suggests that the reaction on the frozen solution is occurring with the associated brine, and not with the ice bulk or a quasi-liquid layer existing on the ice. The implications of these results to bromine activation in the tropospheric boundary layer are made.}, + pages = {2590--2598}, + number = {12}, + journaltitle = {The Journal of Physical Chemistry A}, + shortjournal = {J. Phys. Chem. A}, + author = {Oldridge, N. W. and Abbatt, J. P. D.}, + urldate = {2025-12-21}, + date = {2011-03-31}, + note = {Publisher: American Chemical Society}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/NIUXDZB5/Oldridge and Abbatt - 2011 - Formation of Gas-Phase Bromine from Interaction of Ozone with Frozen and Liquid NaClNaBr Solutions.pdf:application/pdf}, +} + +@article{saunders_insights_2012, + title = {Insights into the Photochemical Transformation of Iodine in Aqueous Systems: Humic Acid Photosensitized Reduction of Iodate}, + volume = {46}, + issn = {0013-936X}, + url = {https://doi.org/10.1021/es3030935}, + doi = {10.1021/es3030935}, + shorttitle = {Insights into the Photochemical Transformation of Iodine in Aqueous Systems}, + abstract = {Marine aerosol is highly enriched in iodine, mostly in the form of iodate ({IO}3–) ions, compared to its relative abundance in seawater. This paper describes a laboratory study of the photochemical reduction of {IO}3– in the presence of humic acid. Spectroscopic analysis showed that ∼20\% of {IO}3– was converted to “free” iodide (I–) ions and this fraction remained constant as a function of time. Direct detection of an organically fixed fraction (i.e., ∼ 80\%) was not possible, but a number of test reactions with surrogate organic compounds containing functional groups identified in humic acid structures indicate that efficient substitution of iodine occurs at aromatic 1,2 diol sites. These iodinated humic acids are stable with respect to photolysis at near-{UV}/visible wavelengths and are likely to account for a significant proportion of the soluble iodine-containing organic material occurring within aerosols. In the lower atmosphere, oxidation of I– to I2 in marine aerosol occurs mostly through the uptake of O3, with H2O2 playing a very minor role. A model of iodine chemistry in the open ocean tropical boundary layer, which incorporates these experimental results, is able to account for the observed enrichment of iodine in marine aerosol.}, + pages = {11854--11861}, + number = {21}, + journaltitle = {Environmental Science \& Technology}, + shortjournal = {Environ. Sci. Technol.}, + author = {Saunders, Russell W. and Kumar, Ravi and {MacDonald}, Samantha M. and Plane, John M. C.}, + urldate = {2025-12-21}, + date = {2012-11-06}, + note = {Publisher: American Chemical Society}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/IZ68AN68/Saunders et al. - 2012 - Insights into the Photochemical Transformation of Iodine in Aqueous Systems Humic Acid Photosensiti.pdf:application/pdf}, +} + +@article{spokes_photochemically_1996, + title = {Photochemically induced redox reactions in seawater, {II}. Nitrogen and iodine}, + volume = {54}, + issn = {0304-4203}, + url = {https://www.sciencedirect.com/science/article/pii/0304420396000333}, + doi = {10.1016/0304-4203(96)00033-3}, + abstract = {Experiments have been conducted to determine whether the speciation of the nitrate-nitrite and iodate-iodide redox couples is influenced by light and organic matter in both deionised and sea waters. The results obtained indicate that photochemical production of nitrite occurs and that the rate of this reaction is dependent on the concentration of organic matter present in the system. The findings suggest that nitrate undergoes not only direct photochemical reaction, acting itself as a primary chromophore, but also a photochemically induced reduction through organic matter. This reaction is, however, unlikely to influence productivity to any great extent as most phytoplankton can use both species as nutrients. It may, however, be a source of the highly reactive hydroxyl radical and of {NO} which has the potential to degas to the atmosphere and there help to regulate ozone concentration. Experiments conducted on the iodine redox system similarly indicate that photochemically induced production of iodide occurs. The results show that the reaction is not biologically mediated and that the presence of organic matter is essential for iodide photoproduction. At the concentrations of added iodate used in the experiments no direct 1:1 relationship between iodate and iodide is seen. It is suggested that, under these conditions, organic matter is not only essential for the photochemical production of iodide but that it is also the limiting species for the reduction reaction.}, + pages = {1--10}, + number = {1}, + journaltitle = {Marine Chemistry}, + shortjournal = {Marine Chemistry}, + author = {Spokes, Lucinda J. and Liss, Peter S.}, + urldate = {2025-12-21}, + date = {1996-09-01}, + file = {PDF:/Users/davidtschan/Zotero/storage/2URDLBAC/Spokes and Liss - 1996 - Photochemically induced redox reactions in seawater, II. Nitrogen and iodine.pdf:application/pdf;ScienceDirect Snapshot:/Users/davidtschan/Zotero/storage/7QHIHCLU/0304420396000333.html:text/html}, +} + +@article{aguer_effect_1999, + title = {Effect of light on humic substances : production of reactive species}, + volume = {27}, + issn = {0365-4877, 1286-482X}, + url = {http://analusis.edpsciences.org/10.1051/analusis:1999270387}, + doi = {10.1051/analusis:1999270387}, + shorttitle = {Effect of light on humic substances}, + pages = {387--389}, + number = {5}, + journaltitle = {Analusis}, + shortjournal = {Analusis}, + author = {Aguer, J. P. and Richard, C. and Andreux, F.}, + urldate = {2025-12-21}, + date = {1999-06}, + langid = {english}, + file = {PDF:/Users/davidtschan/Zotero/storage/7D4FCQFF/Aguer et al. - 1999 - Effect of light on humic substances production of reactive species.pdf:application/pdf}, +} + +@article{baker_marine_2005, + title = {Marine Aerosol Iodine Chemistry: The Importance of Soluble Organic Iodine}, + volume = {2}, + issn = {1448-2517}, + url = {https://doi.org/10.1071/EN05070}, + doi = {10.1071/EN05070}, + shorttitle = {Marine Aerosol Iodine Chemistry}, + abstract = {Environmental Context. Ozone concentrations play a large part in controlling the oxidation capacity of the marine boundary layer, while the production of new aerosol particles affects atmospheric radiative balance. Iodine has a complex chemistry in the marine atmosphere which impacts on both these processes. Much of this iodine chemistry, especially the chemical speciation of iodine in aerosol, is only poorly understood. This study explores the occurrence and abundance of organic forms of iodine, a topic that has received very little attention to date.Abstract. Iodine has a complex chemistry in aerosols in the marine boundary layer ({MBL}), and is involved in both ozone destruction and new aerosol particle formation processes. Work in this area has focussed almost exclusively on inorganic iodine chemistry. Results from two research cruises in the Atlantic Ocean, covering wide longitude (60°W to 0°W) and latitude (50°N to 50°S) ranges indicate that soluble organic iodine species are both widespread and abundant in marine aerosol. The reactivity of these species is yet to be determined, but may influence the concentrations of some aerosol inorganic iodine species, and may also impact on {MBL} ozone destruction reactions.}, + pages = {295--298}, + number = {4}, + journaltitle = {Environmental Chemistry}, + shortjournal = {Environ Chem}, + author = {Baker, Alex R.}, + urldate = {2025-12-21}, + date = {2005-12-08}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/8YR6TBK7/Baker - 2005 - Marine Aerosol Iodine Chemistry The Importance of Soluble Organic Iodine.pdf:application/pdf;Snapshot:/Users/davidtschan/Zotero/storage/7WB8LECK/EN05070.html:text/html}, +} + +@article{cooper_photochemical_1988, + title = {Photochemical formation of hydrogen peroxide in natural waters exposed to sunlight}, + volume = {22}, + issn = {0013-936X}, + url = {https://doi.org/10.1021/es00175a004}, + doi = {10.1021/es00175a004}, + pages = {1156--1160}, + number = {10}, + journaltitle = {Environmental Science \& Technology}, + shortjournal = {Environ. Sci. Technol.}, + author = {Cooper, William J. and Zika, Rod G. and Petasne, Robert G. and Plane, John M. C.}, + urldate = {2025-12-21}, + date = {1988-10-01}, + note = {Publisher: American Chemical Society}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/8DDDFXRB/Cooper et al. - 1988 - Photochemical formation of hydrogen peroxide in natural waters exposed to sunlight.pdf:application/pdf}, +} + +@article{graber_atmospheric_2006, + title = {Atmospheric {HULIS}: How humic-like are they? A comprehensive and critical review}, + volume = {6}, + issn = {1680-7316}, + url = {https://acp.copernicus.org/articles/6/729/2006/}, + doi = {10.5194/acp-6-729-2006}, + shorttitle = {Atmospheric {HULIS}}, + abstract = {A class of organic molecules extracted from atmospheric aerosol particles and isolated from fog and cloud water has been termed {HUmic}-{LIke} Substances ({HULIS}) due to a certain resemblance to terrestrial and aquatic humic and fulvic acids. In light of the interest that this class of atmospheric compounds currently attracts, we comprehensively review {HULIS} properties, as well as laboratory and field investigations concerning their formation and characterization in atmospheric samples. While sharing some important features such as polyacidic nature, accumulating\ evidence suggests that atmospheric {HULIS} differ substantially from\ terrestrial and aquatic humic substances. Major differences between {HULIS} and humic substances, including smaller average molecular weight, lower aromatic moiety content, greater surface activity, better droplet activation ability, as well as others, are highlighted. Several alternatives are proposed that may explain such differences: (1) the possibility that mono- and di-carboxylic acids and mineral acids abundant in the atmosphere prevent the formation of large humic "supramolecular associations"; (2) that large humic macromolecules are destroyed in the atmosphere by {UV} radiation, O3, and {OH}- radicals; (3) that "{HULIS}" actually consists of a complex, unresolved mixture of relatively small molecules rather than macromolecular entities; and (4) that {HULIS} formed via abiotic and short-lived oxidative reaction pathways differ substantially from humic substances formed over long time periods via biologically-mediated reactions. It should also be recalled that the vast majority of studies of {HULIS} relate to the water soluble fraction, which would include only the fulvic acid fraction of humic substances, and exclude the humic acid (base-soluble) and humin (insoluble) fractions of humic substances. A significant effort towards adopting standard extraction and characterization methods is required to develop a better and meaningful comparison between different {HULIS} samples.}, + pages = {729--753}, + number = {3}, + journaltitle = {Atmospheric Chemistry and Physics}, + author = {Graber, E. R. and Rudich, Y.}, + urldate = {2025-12-21}, + date = {2006-03-06}, + note = {Publisher: Copernicus {GmbH}}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/6CL4KKX7/Graber and Rudich - 2006 - Atmospheric HULIS How humic-like are they A comprehensive and critical review.pdf:application/pdf}, +} + +@article{aal-abadleh_perspective_2023, + title = {A perspective on iron (Fe) in the atmosphere: air quality, climate, and the ocean}, + volume = {25}, + url = {https://pubs.rsc.org/en/content/articlelanding/2023/em/d2em00176d}, + doi = {10.1039/D2EM00176D}, + shorttitle = {A perspective on iron (Fe) in the atmosphere}, + pages = {151--164}, + number = {2}, + journaltitle = {Environmental Science: Processes \& Impacts}, + author = {A. Al-Abadleh, Hind and D. Kubicki, James and Meskhidze, Nicholas}, + urldate = {2025-12-21}, + date = {2023}, + langid = {english}, + note = {Publisher: Royal Society of Chemistry}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/Z5AWY5F9/A. Al-Abadleh et al. - 2023 - A perspective on iron (Fe) in the atmosphere air quality, climate, and the ocean.pdf:application/pdf}, +} + +@article{dou_photochemical_2021, + title = {Photochemical degradation of iron({III}) citrate/citric acid aerosol quantified with the combination of three complementary experimental techniques and a kinetic process model}, + volume = {21}, + issn = {1680-7316}, + url = {https://acp.copernicus.org/articles/21/315/2021/}, + doi = {10.5194/acp-21-315-2021}, + abstract = {Iron({III}) carboxylate photochemistry plays an important role in aerosol aging, especially in the lower troposphere. These complexes can absorb light over a broad wavelength range, inducing the reduction of iron({III}) and the oxidation of carboxylate ligands. In the presence of O2, the ensuing radical chemistry leads to further decarboxylation, and the production of .{OH}, {HO}2., peroxides, and oxygenated volatile organic compounds, contributing to particle mass loss. The .{OH}, {HO}2., and peroxides in turn reoxidize iron({II}) back to iron({III}), closing a photocatalytic cycle. This cycle is repeated, resulting in continual mass loss due to the release of {CO}2 and other volatile compounds. In a cold and/or dry atmosphere, organic aerosol particles tend to attain highly viscous states. While the impact of reduced mobility of aerosol constituents on dark chemical reactions has received substantial attention, studies on the effect of high viscosity on photochemical processes are scarce. Here, we choose iron({III}) citrate ({FeIII}(Cit)) as a model light-absorbing iron carboxylate complex that induces citric acid ({CA}) degradation to investigate how transport limitations influence photochemical processes. Three complementary experimental approaches were used to investigate kinetic transport limitations. The mass loss of single, levitated particles was measured with an electrodynamic balance, the oxidation state of deposited particles was measured with X-ray spectromicroscopy, and {HO}2. radical production and release into the gas phase was observed in coated-wall flow-tube experiments. We observed significant photochemical degradation with up to 80 \% mass loss within 24 h of light exposure. Interestingly, we also observed that mass loss always accelerated during irradiation, resulting in an increase of the mass loss rate by about a factor of 10. When we increased relative humidity ({RH}), the observed particle mass loss rate also increased. This is consistent with strong kinetic transport limitations for highly viscous particles. To quantitatively compare these experiments and determine important physical and chemical parameters, a numerical multilayered photochemical reaction and diffusion ({PRAD}) model was developed that treats chemical reactions and the transport of various species. The {PRAD} model was tuned to simultaneously reproduce all experimental results as closely as possible and captured the essential chemistry and transport during irradiation. In particular, the photolysis rate of {FeIII}, the reoxidation rate of {FeII}, {HO}2. production, and the diffusivity of O2 in aqueous {FeIII}(Cit) ∕ {CA} system as function of {RH} and {FeIII}(Cit) ∕ {CA} molar ratio could be constrained. This led to satisfactory agreement within model uncertainty for most but not all experiments performed. Photochemical degradation under atmospheric conditions predicted by the {PRAD} model shows that release of {CO}2 and repartitioning of organic compounds to the gas phase may be very important when attempting to accurately predict organic aerosol aging processes.}, + pages = {315--338}, + number = {1}, + journaltitle = {Atmospheric Chemistry and Physics}, + author = {Dou, Jing and Alpert, Peter A. and Corral Arroyo, Pablo and Luo, Beiping and Schneider, Frederic and Xto, Jacinta and Huthwelker, Thomas and Borca, Camelia N. and Henzler, Katja D. and Raabe, Jörg and Watts, Benjamin and Herrmann, Hartmut and Peter, Thomas and Ammann, Markus and Krieger, Ulrich K.}, + urldate = {2025-12-21}, + date = {2021-01-13}, + note = {Publisher: Copernicus {GmbH}}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/B9FMPQAB/Dou et al. - 2021 - Photochemical degradation of iron(III) citratecitric acid aerosol quantified with the combination o.pdf:application/pdf}, +} + +@article{crounse_autoxidation_2013, + title = {Autoxidation of Organic Compounds in the Atmosphere}, + volume = {4}, + url = {https://doi.org/10.1021/jz4019207}, + doi = {10.1021/jz4019207}, + abstract = {We present a hypothesis that autoxidation (inter- and intramolecular hydrogen abstraction by peroxy radicals) plays an important role in the oxidation of organic compounds in the atmosphere, particularly organic matter associated with aerosol. In the laboratory, we determine the rate of this process at room temperature for a model system, 3-pentanone. We employ ab initio calculations to investigate H-shifts within a broader group of substituted organic compounds. We show that the rate of abstraction of hydrogen by peroxy radicals is largely determined by the thermochemistry of the nascent alkyl radicals and thus is highly influenced by neighboring substituents. As a result, autoxidation rates increase rapidly as oxygen-containing functional groups (carbonyl, hydroxy, and hydroperoxy) are added to organic compounds. This mechanism is consistent with formation of the multifunctional hydroperoxides and carbonyls often found in atmospheric aerosol particles.}, + pages = {3513--3520}, + number = {20}, + journaltitle = {The Journal of Physical Chemistry Letters}, + shortjournal = {J. Phys. Chem. Lett.}, + author = {Crounse, John D. and Nielsen, Lasse B. and Jørgensen, Solvejg and Kjaergaard, Henrik G. and Wennberg, Paul O.}, + urldate = {2025-12-21}, + date = {2013-10-17}, + note = {Publisher: American Chemical Society}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/22VDR2GC/Crounse et al. - 2013 - Autoxidation of Organic Compounds in the Atmosphere.pdf:application/pdf}, +} + +@article{bell_sensitivity_2023, + title = {Sensitivity Constraints of Extractive Electrospray for a Model System and Secondary Organic Aerosol}, + volume = {95}, + issn = {0003-2700}, + url = {https://doi.org/10.1021/acs.analchem.3c00441}, + doi = {10.1021/acs.analchem.3c00441}, + abstract = {The quantification of an aerosol chemical composition is complicated by the uncertainty in the sensitivity of each species detected. Soft-ionization response factors can vary widely from molecule to molecule. Here, we have employed a method to separate molecules by their volatility through systematic evaporation with a thermal denuder ({TD}). The fraction remaining after evaporation is compared between an extractive electrospray ionization time-of-flight mass spectrometer ({EESI}-{TOF}) and a scanning mobility particle sizer ({SMPS}), which provides a comparison between a quantified mass loss by the {SMPS} and the signal loss in the {EESI}-{TOF}. The sensitivity of the {EESI}-{TOF} is determined for both a simplified complex mixture ({PEG}-300) and also for a complex mixture of α-pinene secondary organic aerosol ({SOA}). For {PEG}-300, separation is possible on a molecule-by-molecule level with the {TD} and provides insights into the molecule-dependent sensitivity of the {EESI}-{TOF}, showing a higher sensitivity toward the most volatile molecule. For α-pinene {SOA}, sensitivity determination for specific classes is possible because of the number of molecular formula observed by the {EESI}-{TOF}. These classes are separated by their volatility and are broken down into monomers (O3–5,6–7,8+), dimers (O4–7,8+), and higher order oligomers (e.g., trimers and tetramers). Here, we show that the {EESI}-{TOF} initially measures 60.1\% monomers, 32.7\% dimers, and 7.2\% trimers and tetramers in α-pinene {SOA}, but after sensitivity correction, the distribution of {SOA} is 37.4\% monomers, 56.1\% dimers, and 6.4\% trimers and tetramers. These results provide a path forward for the quantification of aerosol components with the {EESI}-{TOF} in other applications and potentially for atmospheric measurements.}, + pages = {13788--13795}, + number = {37}, + journaltitle = {Analytical Chemistry}, + shortjournal = {Anal. Chem.}, + author = {Bell, David M. and Zhang, Jun and Top, Jens and Bogler, Sophie and Surdu, Mihnea and Slowik, Jay G. and Prevot, Andre S. H. and El Haddad, Imad}, + urldate = {2025-12-21}, + date = {2023-09-19}, + note = {Publisher: American Chemical Society}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/PGANZJH2/Bell et al. - 2023 - Sensitivity Constraints of Extractive Electrospray for a Model System and Secondary Organic Aerosol.pdf:application/pdf}, +} + +@article{carlton_review_2009, + title = {A review of Secondary Organic Aerosol ({SOA}) formation from isoprene}, + volume = {9}, + issn = {1680-7316}, + url = {https://acp.copernicus.org/articles/9/4987/2009/}, + doi = {10.5194/acp-9-4987-2009}, + abstract = {Recent field and laboratory evidence indicates that the oxidation of isoprene, (2-methyl-1,3-butadiene, C5H8) forms secondary organic aerosol ({SOA}). Global biogenic emissions of isoprene (600 Tg yr\−1) are sufficiently large that the formation of {SOA} in even small yields results in substantial production of atmospheric particulate matter, likely having implications for air quality and climate. Here we present a review of field measurements, experimental work, and modeling studies aimed at understanding the mechanisms, yield, and atmospheric importance of isoprene-derived {SOA}. {SOA} yields depend on a number of factors, including organic aerosol loading (Mo), {NOx} level ({RO}2 chemistry), and, because of the importance of multigenerational chemistry, the degree of oxidation. These dependences are not always included in {SOA} modules used in atmospheric transport models, and instead most yield parameterizations rely on a single set of chamber experiments (carried out over a limited range of conditions); this may lead to very different estimates of the atmospheric importance of isoprene {SOA}. New yield parameterizations, based on all available laboratory data (Mo=0–50 μg m\−3), are presented here, so that {SOA} formation may be computed as a function of Mo, {NOx} level, and temperature. Current research needs and future research directions are identified.}, + pages = {4987--5005}, + number = {14}, + journaltitle = {Atmospheric Chemistry and Physics}, + author = {Carlton, A. G. and Wiedinmyer, C. and Kroll, J. H.}, + urldate = {2025-12-21}, + date = {2009-07-27}, + note = {Publisher: Copernicus {GmbH}}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/K2TYY3XI/Carlton et al. - 2009 - A review of Secondary Organic Aerosol (SOA) formation from isoprene.pdf:application/pdf}, +} + +@article{guenther_estimates_2006, + title = {Estimates of global terrestrial isoprene emissions using {MEGAN} (Model of Emissions of Gases and Aerosols from Nature)}, + volume = {6}, + issn = {1680-7316}, + url = {https://acp.copernicus.org/articles/6/3181/2006/}, + doi = {10.5194/acp-6-3181-2006}, + abstract = {Reactive gases and aerosols are produced by terrestrial ecosystems, processed within plant canopies, and can then be emitted into the above-canopy atmosphere. Estimates of the above-canopy fluxes are needed for quantitative earth system studies and assessments of past, present and future air quality and climate. The Model of Emissions of Gases and Aerosols from Nature ({MEGAN}) is described and used to quantify net terrestrial biosphere emission of isoprene into the atmosphere. {MEGAN} is designed for both global and regional emission modeling and has global coverage with {\textasciitilde}1 km2 spatial resolution. Field and laboratory investigations of the processes controlling isoprene emission are described and data available for model development and evaluation are summarized. The factors controlling isoprene emissions include biological, physical and chemical driving variables. {MEGAN} driving variables are derived from models and satellite and ground observations. Tropical broadleaf trees contribute almost half of the estimated global annual isoprene emission due to their relatively high emission factors and because they are often exposed to conditions that are conducive for isoprene emission. The remaining flux is primarily from shrubs which have a widespread distribution. The annual global isoprene emission estimated with {MEGAN} ranges from about 500 to 750 Tg isoprene (440 to 660 Tg carbon) depending on the driving variables which include temperature, solar radiation, Leaf Area Index, and plant functional type. The global annual isoprene emission estimated using the standard driving variables is {\textasciitilde}600 Tg isoprene. Differences in driving variables result in emission estimates that differ by more than a factor of three for specific times and locations. It is difficult to evaluate isoprene emission estimates using the concentration distributions simulated using chemistry and transport models, due to the substantial uncertainties in other model components, but at least some global models produce reasonable results when using isoprene emission distributions similar to {MEGAN} estimates. In addition, comparison with isoprene emissions estimated from satellite formaldehyde observations indicates reasonable agreement. The sensitivity of isoprene emissions to earth system changes (e.g., climate and land-use) demonstrates the potential for large future changes in emissions. Using temperature distributions simulated by global climate models for year 2100, {MEGAN} estimates that isoprene emissions increase by more than a factor of two. This is considerably greater than previous estimates and additional observations are needed to evaluate and improve the methods used to predict future isoprene emissions.}, + pages = {3181--3210}, + number = {11}, + journaltitle = {Atmospheric Chemistry and Physics}, + author = {Guenther, A. and Karl, T. and Harley, P. and Wiedinmyer, C. and Palmer, P. I. and Geron, C.}, + urldate = {2025-12-21}, + date = {2006-08-02}, + note = {Publisher: Copernicus {GmbH}}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/2ZJBQFMF/Guenther et al. - 2006 - Estimates of global terrestrial isoprene emissions using MEGAN (Model of Emissions of Gases and Aero.pdf:application/pdf}, +} + +@article{atkinson_atmospheric_2003, + title = {Atmospheric Degradation of Volatile Organic Compounds}, + volume = {103}, + issn = {0009-2665}, + url = {https://doi.org/10.1021/cr0206420}, + doi = {10.1021/cr0206420}, + pages = {4605--4638}, + number = {12}, + journaltitle = {Chemical Reviews}, + shortjournal = {Chem. Rev.}, + author = {Atkinson, Roger and Arey, Janet}, + urldate = {2025-12-21}, + date = {2003-12-01}, + note = {Publisher: American Chemical Society}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/4TE8ABLY/Atkinson and Arey - 2003 - Atmospheric Degradation of Volatile Organic Compounds.pdf:application/pdf}, +} + +@article{guenther_global_1995, + title = {A global model of natural volatile organic compound emissions}, + volume = {100}, + rights = {Copyright 1995 by the American Geophysical Union.}, + issn = {2156-2202}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1029/94JD02950}, + doi = {10.1029/94JD02950}, + abstract = {Numerical assessments of global air quality and potential changes in atmospheric chemical constituents require estimates of the surface fluxes of a variety of trace gas species. We have developed a global model to estimate emissions of volatile organic compounds from natural sources ({NVOC}). Methane is not considered here and has been reviewed in detail elsewhere. The model has a highly resolved spatial grid (0.5°×0.5° latitude/longitude) and generates hourly average emission estimates. Chemical species are grouped into four categories: isoprene, monoterpenes, other reactive {VOC} ({ORVOC}), and other {VOC} ({OVOC}). {NVOC} emissions from oceans are estimated as a function of geophysical variables from a general circulation model and ocean color satellite data. Emissions from plant foliage are estimated from ecosystem specific biomass and emission factors and algorithms describing light and temperature dependence of {NVOC} emissions. Foliar density estimates are based on climatic variables and satellite data. Temporal variations in the model are driven by monthly estimates of biomass and temperature and hourly light estimates. The annual global {VOC} flux is estimated to be 1150 Tg C, composed of 44\% isoprene, 11\% monoterpenes, 22.5\% other reactive {VOC}, and 22.5\% other {VOC}. Large uncertainties exist for each of these estimates and particularly for compounds other than isoprene and monoterpenes. Tropical woodlands (rain forest, seasonal, drought-deciduous, and savanna) contribute about half of all global natural {VOC} emissions. Croplands, shrublands and other woodlands contribute 10–20\% apiece. Isoprene emissions calculated for temperate regions are as much as a factor of 5 higher than previous estimates.}, + pages = {8873--8892}, + issue = {D5}, + journaltitle = {Journal of Geophysical Research: Atmospheres}, + author = {Guenther, Alex and Hewitt, C. Nicholas and Erickson, David and Fall, Ray and Geron, Chris and Graedel, Tom and Harley, Peter and Klinger, Lee and Lerdau, Manuel and Mckay, W. A. and Pierce, Tom and Scholes, Bob and Steinbrecher, Rainer and Tallamraju, Raja and Taylor, John and Zimmerman, Pat}, + urldate = {2025-12-21}, + date = {1995}, + langid = {english}, + note = {\_eprint: https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/94JD02950}, + file = {Full Text:/Users/davidtschan/Zotero/storage/JST7UPGY/Guenther et al. - 1995 - A global model of natural volatile organic compound emissions.pdf:application/pdf;Snapshot:/Users/davidtschan/Zotero/storage/VLDMRIRM/94JD02950.html:text/html}, +} + +@article{guenther_model_2012, + title = {The Model of Emissions of Gases and Aerosols from Nature version 2.1 ({MEGAN}2.1): an extended and updated framework for modeling biogenic emissions}, + volume = {5}, + issn = {1991-959X}, + url = {https://gmd.copernicus.org/articles/5/1471/2012/}, + doi = {10.5194/gmd-5-1471-2012}, + shorttitle = {The Model of Emissions of Gases and Aerosols from Nature version 2.1 ({MEGAN}2.1)}, + abstract = {The Model of Emissions of Gases and Aerosols from Nature version 2.1 ({MEGAN}2.1) is a modeling framework for estimating fluxes of biogenic compounds between terrestrial ecosystems and the atmosphere using simple mechanistic algorithms to account for the major known processes controlling biogenic emissions. It is available as an offline code and has also been coupled into land surface and atmospheric chemistry models. {MEGAN}2.1 is an update from the previous versions including {MEGAN}2.0, which was described for isoprene emissions by Guenther et al. (2006) and {MEGAN}2.02, which was described for monoterpene and sesquiterpene emissions by Sakulyanontvittaya et al. (2008). Isoprene comprises about half of the total global biogenic volatile organic compound ({BVOC}) emission of 1 Pg (1000 Tg or 1015 g) estimated using {MEGAN}2.1. Methanol, ethanol, acetaldehyde, acetone, α-pinene, β-pinene, t-β-ocimene, limonene, ethene, and propene together contribute another 30\% of the {MEGAN}2.1 estimated emission. An additional 20 compounds (mostly terpenoids) are associated with the {MEGAN}2.1 estimates of another 17\% of the total emission with the remaining 3\% distributed among {\textgreater}100 compounds. Emissions of 41 monoterpenes and 32 sesquiterpenes together comprise about 15\% and 3\%, respectively, of the estimated total global {BVOC} emission. Tropical trees cover about 18\% of the global land surface and are estimated to be responsible for {\textasciitilde}80\% of terpenoid emissions and {\textasciitilde}50\% of other {VOC} emissions. Other trees cover about the same area but are estimated to contribute only about 10\% of total emissions. The magnitude of the emissions estimated with {MEGAN}2.1 are within the range of estimates reported using other approaches and much of the differences between reported values can be attributed to land cover and meteorological driving variables. The offline version of {MEGAN}2.1 source code and driving variables is available from http://bai.acd.ucar.edu/{MEGAN}/ and the version integrated into the Community Land Model version 4 ({CLM}4) can be downloaded from http://www.cesm.ucar.edu/.}, + pages = {1471--1492}, + number = {6}, + journaltitle = {Geoscientific Model Development}, + author = {Guenther, A. B. and Jiang, X. and Heald, C. L. and Sakulyanontvittaya, T. and Duhl, T. and Emmons, L. K. and Wang, X.}, + urldate = {2025-12-21}, + date = {2012-11-26}, + note = {Publisher: Copernicus {GmbH}}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/ACA4W5KU/Guenther et al. - 2012 - The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1) an extended and upd.pdf:application/pdf}, +} + +@article{donahue_atmospheric_2009, + title = {Atmospheric organic particulate matter: From smoke to secondary organic aerosol}, + volume = {43}, + issn = {1352-2310}, + url = {https://www.sciencedirect.com/science/article/pii/S1352231008009229}, + doi = {10.1016/j.atmosenv.2008.09.055}, + series = {Atmospheric Environment - Fifty Years of Endeavour}, + shorttitle = {Atmospheric organic particulate matter}, + abstract = {We present an overview of the development of our understanding of the sources, formation mechanisms, physical and chemical transformations of atmospheric organic aerosol ({OA}) during the last thirty years. Until recently, organic particulate material was simply classified as either primary or secondary with the primary component being treated in models as nonvolatile and inert. However, this oversimplified view fails to explain the highly oxygenated nature of ambient {OA}, the relatively small {OA} concentration gradients between urban areas and their surroundings, and the concentrations of {OA} during periods of high photochemical activity. A unifying framework for the description of all components based on their volatility distribution (the volatility basis set) can be used for the treatment of a wide range of processes affecting organic aerosol loadings and composition in the atmosphere. These processes include direct organic particle and vapor emissions, chemical production of organic {PM} from volatile precursors, chemical reactions (aging) in all phases, as well as deposition of both particles and vapors and chemical losses to volatile products. The combination of this new framework with the recent results of laboratory studies can resolve some of the discrepancies between {OA} observations and laboratory results. The mass balance of the organic material as a function of its volatility is investigated and used to frame the corresponding constraints on the system. Finally we revisit the traditional definitions of primary and secondary organic aerosol and propose a new set of terms and definitions based on the improvements of our understanding.}, + pages = {94--106}, + number = {1}, + journaltitle = {Atmospheric Environment}, + shortjournal = {Atmospheric Environment}, + author = {Donahue, Neil M. and Robinson, Allen L. and Pandis, Spyros N.}, + urldate = {2025-12-21}, + date = {2009-01-01}, + file = {PDF:/Users/davidtschan/Zotero/storage/37UK4JXS/Donahue et al. - 2009 - Atmospheric organic particulate matter From smoke to secondary organic aerosol.pdf:application/pdf;ScienceDirect Snapshot:/Users/davidtschan/Zotero/storage/6H3RB3QL/S1352231008009229.html:text/html}, +} + +@article{hallquist_formation_2009, + title = {The formation, properties and impact of secondary organic aerosol: current and emerging issues}, + volume = {9}, + issn = {1680-7316}, + url = {https://acp.copernicus.org/articles/9/5155/2009/}, + doi = {10.5194/acp-9-5155-2009}, + shorttitle = {The formation, properties and impact of secondary organic aerosol}, + abstract = {Secondary organic aerosol ({SOA}) accounts for a significant fraction of ambient tropospheric aerosol and a detailed knowledge of the formation, properties and transformation of {SOA} is therefore required to evaluate its impact on atmospheric processes, climate and human health. The chemical and physical processes associated with {SOA} formation are complex and varied, and, despite considerable progress in recent years, a quantitative and predictive understanding of {SOA} formation does not exist and therefore represents a major research challenge in atmospheric science. This review begins with an update on the current state of knowledge on the global {SOA} budget and is followed by an overview of the atmospheric degradation mechanisms for {SOA} precursors, gas-particle partitioning theory and the analytical techniques used to determine the chemical composition of {SOA}. A survey of recent laboratory, field and modeling studies is also presented. The following topical and emerging issues are highlighted and discussed in detail: molecular characterization of biogenic {SOA} constituents, condensed phase reactions and oligomerization, the interaction of atmospheric organic components with sulfuric acid, the chemical and photochemical processing of organics in the atmospheric aqueous phase, aerosol formation from real plant emissions, interaction of atmospheric organic components with water, thermodynamics and mixtures in atmospheric models. Finally, the major challenges ahead in laboratory, field and modeling studies of {SOA} are discussed and recommendations for future research directions are proposed.}, + pages = {5155--5236}, + number = {14}, + journaltitle = {Atmospheric Chemistry and Physics}, + author = {Hallquist, M. and Wenger, J. C. and Baltensperger, U. and Rudich, Y. and Simpson, D. and Claeys, M. and Dommen, J. and Donahue, N. M. and George, C. and Goldstein, A. H. and Hamilton, J. F. and Herrmann, H. and Hoffmann, T. and Iinuma, Y. and Jang, M. and Jenkin, M. E. and Jimenez, J. L. and Kiendler-Scharr, A. and Maenhaut, W. and {McFiggans}, G. and Mentel, Th F. and Monod, A. and Prévôt, A. S. H. and Seinfeld, J. H. and Surratt, J. D. and Szmigielski, R. and Wildt, J.}, + urldate = {2025-12-21}, + date = {2009-07-29}, + note = {Publisher: Copernicus {GmbH}}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/D2GMK6BZ/Hallquist et al. - 2009 - The formation, properties and impact of secondary organic aerosol current and emerging issues.pdf:application/pdf}, +} + +@article{ehn_large_2014, + title = {A large source of low-volatility secondary organic aerosol}, + volume = {506}, + rights = {2014 Springer Nature Limited}, + issn = {1476-4687}, + url = {https://www.nature.com/articles/nature13032}, + doi = {10.1038/nature13032}, + abstract = {The link between biogenic volatile organic compounds in the atmosphere and their conversion to aerosol particles is unclear, but a direct reaction pathway is now described by which volatile organic compounds lead to low-volatility vapours that can then condense onto aerosol surfaces, producing secondary organic aerosol.}, + pages = {476--479}, + number = {7489}, + journaltitle = {Nature}, + author = {Ehn, Mikael and Thornton, Joel A. and Kleist, Einhard and Sipilä, Mikko and Junninen, Heikki and Pullinen, Iida and Springer, Monika and Rubach, Florian and Tillmann, Ralf and Lee, Ben and Lopez-Hilfiker, Felipe and Andres, Stefanie and Acir, Ismail-Hakki and Rissanen, Matti and Jokinen, Tuija and Schobesberger, Siegfried and Kangasluoma, Juha and Kontkanen, Jenni and Nieminen, Tuomo and Kurtén, Theo and Nielsen, Lasse B. and Jørgensen, Solvejg and Kjaergaard, Henrik G. and Canagaratna, Manjula and Maso, Miikka Dal and Berndt, Torsten and Petäjä, Tuukka and Wahner, Andreas and Kerminen, Veli-Matti and Kulmala, Markku and Worsnop, Douglas R. and Wildt, Jürgen and Mentel, Thomas F.}, + urldate = {2025-12-21}, + date = {2014-02}, + langid = {english}, + note = {Publisher: Nature Publishing Group}, + keywords = {Atmospheric chemistry}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/K84688XX/Ehn et al. - 2014 - A large source of low-volatility secondary organic aerosol.pdf:application/pdf}, +} + +@article{jokinen_production_2015, + title = {Production of extremely low volatile organic compounds from biogenic emissions: Measured yields and atmospheric implications}, + volume = {112}, + url = {https://www.pnas.org/doi/abs/10.1073/pnas.1423977112}, + doi = {10.1073/pnas.1423977112}, + shorttitle = {Production of extremely low volatile organic compounds from biogenic emissions}, + abstract = {Oxidation products of monoterpenes and isoprene have a major influence on the global +secondary organic aerosol ({SOA}) burden and the production of a...}, + pages = {7123--7128}, + number = {23}, + journaltitle = {Proceedings of the National Academy of Sciences}, + author = {Jokinen, Tuija and Berndt, Torsten and Makkonen, Risto and Kerminen, Veli-Matti and Junninen, Heikki and Paasonen, Pauli and Stratmann, Frank and Herrmann, Hartmut and Guenther, Alex B. and Worsnop, Douglas R. and Kulmala, Markku and Ehn, Mikael and Sipilä, Mikko}, + urldate = {2025-12-21}, + date = {2015-06-09}, + note = {Company: National Academy of Sciences +Distributor: National Academy of Sciences +Institution: National Academy of Sciences +Label: National Academy of Sciences +Publisher: Proceedings of the National Academy of Sciences}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/E67KQE5P/Jokinen et al. - 2015 - Production of extremely low volatile organic compounds from biogenic emissions Measured yields and.pdf:application/pdf}, +} + +@article{ng_secondary_2008, + title = {Secondary organic aerosol ({SOA}) formation from reaction of isoprene with nitrate radicals ({NO}$_{\textrm{3}}$)}, + volume = {8}, + issn = {1680-7316}, + url = {https://acp.copernicus.org/articles/8/4117/2008/}, + doi = {10.5194/acp-8-4117-2008}, + abstract = {Secondary organic aerosol ({SOA}) formation from the reaction of isoprene with nitrate radicals ({NO}3) is investigated in the Caltech indoor chambers. Experiments are performed in the dark and under dry conditions ({RH}\<10\%) using N2O5 as a source of {NO}3 radicals. For an initial isoprene concentration of 18.4 to 101.6 ppb, the {SOA} yield (defined as the ratio of the mass of organic aerosol formed to the mass of parent hydrocarbon reacted) ranges from 4.3\% to 23.8\%. By examining the time evolutions of gas-phase intermediate products and aerosol volume in real time, we are able to constrain the chemistry that leads to the formation of low-volatility products. Although the formation of {ROOR} from the reaction of two peroxy radicals ({RO}2) has generally been considered as a minor channel, based on the gas-phase and aerosol-phase data it appears that {RO}2+{RO}2 reaction (self reaction or cross-reaction) in the gas phase yielding {ROOR} products is a dominant {SOA} formation pathway. A wide array of organic nitrates and peroxides are identified in the aerosol formed and mechanisms for {SOA} formation are proposed. Using a uniform {SOA} yield of 10\% (corresponding to Mo\&\#x2245;10 μg m\−3), it is estimated that {\textasciitilde}2 to 3 Tg yr\−1 of {SOA} results from isoprene+{NO}3. The extent to which the results from this study can be applied to conditions in the atmosphere depends on the fate of peroxy radicals in the nighttime troposphere.}, + pages = {4117--4140}, + number = {14}, + journaltitle = {Atmospheric Chemistry and Physics}, + author = {Ng, N. L. and Kwan, A. J. and Surratt, J. D. and Chan, A. W. H. and Chhabra, P. S. and Sorooshian, A. and Pye, H. O. T. and Crounse, J. D. and Wennberg, P. O. and Flagan, R. C. and Seinfeld, J. H.}, + urldate = {2025-12-21}, + date = {2008-08-01}, + note = {Publisher: Copernicus {GmbH}}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/NTQC2U2Z/Ng et al. - 2008 - Secondary organic aerosol (SOA) formation from reaction of isoprene with nitrate radicals (NO3.pdf:application/pdf}, +} + +@article{kirkby_ion-induced_2016, + title = {Ion-induced nucleation of pure biogenic particles}, + volume = {533}, + rights = {2016 The Author(s)}, + issn = {1476-4687}, + url = {https://www.nature.com/articles/nature17953}, + doi = {10.1038/nature17953}, + abstract = {Aerosol particles can form in the atmosphere by nucleation of highly oxidized biogenic vapours in the absence of sulfuric acid, with ions from Galactic cosmic rays increasing the nucleation rate by one to two orders of magnitude compared with neutral nucleation.}, + pages = {521--526}, + number = {7604}, + journaltitle = {Nature}, + author = {Kirkby, Jasper and Duplissy, Jonathan and Sengupta, Kamalika and Frege, Carla and Gordon, Hamish and Williamson, Christina and Heinritzi, Martin and Simon, Mario and Yan, Chao and Almeida, João and Tröstl, Jasmin and Nieminen, Tuomo and Ortega, Ismael K. and Wagner, Robert and Adamov, Alexey and Amorim, Antonio and Bernhammer, Anne-Kathrin and Bianchi, Federico and Breitenlechner, Martin and Brilke, Sophia and Chen, Xuemeng and Craven, Jill and Dias, Antonio and Ehrhart, Sebastian and Flagan, Richard C. and Franchin, Alessandro and Fuchs, Claudia and Guida, Roberto and Hakala, Jani and Hoyle, Christopher R. and Jokinen, Tuija and Junninen, Heikki and Kangasluoma, Juha and Kim, Jaeseok and Krapf, Manuel and Kürten, Andreas and Laaksonen, Ari and Lehtipalo, Katrianne and Makhmutov, Vladimir and Mathot, Serge and Molteni, Ugo and Onnela, Antti and Peräkylä, Otso and Piel, Felix and Petäjä, Tuukka and Praplan, Arnaud P. and Pringle, Kirsty and Rap, Alexandru and Richards, Nigel A. D. and Riipinen, Ilona and Rissanen, Matti P. and Rondo, Linda and Sarnela, Nina and Schobesberger, Siegfried and Scott, Catherine E. and Seinfeld, John H. and Sipilä, Mikko and Steiner, Gerhard and Stozhkov, Yuri and Stratmann, Frank and Tomé, Antonio and Virtanen, Annele and Vogel, Alexander L. and Wagner, Andrea C. and Wagner, Paul E. and Weingartner, Ernest and Wimmer, Daniela and Winkler, Paul M. and Ye, Penglin and Zhang, Xuan and Hansel, Armin and Dommen, Josef and Donahue, Neil M. and Worsnop, Douglas R. and Baltensperger, Urs and Kulmala, Markku and Carslaw, Kenneth S. and Curtius, Joachim}, + urldate = {2025-12-21}, + date = {2016-05}, + langid = {english}, + note = {Publisher: Nature Publishing Group}, + keywords = {Atmospheric chemistry, Climate-change impacts}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/GFJIG2J5/Kirkby et al. - 2016 - Ion-induced nucleation of pure biogenic particles.pdf:application/pdf}, +} + +@article{lienhard_measurements_2012, + title = {Measurements of Thermodynamic and Optical Properties of Selected Aqueous Organic and Organic–Inorganic Mixtures of Atmospheric Relevance}, + volume = {116}, + issn = {1089-5639}, + url = {https://doi.org/10.1021/jp3055872}, + doi = {10.1021/jp3055872}, + abstract = {Atmospheric aerosol particles can exhibit liquid solution concentrations supersaturated with respect to the dissolved organic and inorganic species and supercooled with respect to ice. In this study, thermodynamic and optical properties of sub- and supersaturated aqueous solutions of atmospheric interest are presented. The density, refractive index, water activity, ice melting temperatures, and homogeneous ice freezing temperatures of binary aqueous solutions containing l(+)-tartaric acid, tannic acid, and levoglucosan and ternary aqueous solutions containing levoglucosan and one of the salts {NH}4HSO4, ({NH}4)2SO4, and {NH}4NO3 have been measured in the supersaturated concentration range for the first time. In addition, the density and refractive index of binary aqueous citric acid and raffinose solutions and the glass transition temperatures of binary aqueous l(+)-tartaric acid and levoglucosan solutions have been measured. The data presented here are derived from experiments on single levitated microdroplets and bulk solutions and should find application in thermodynamic and atmospheric aerosol models as well as in food science applications.}, + pages = {9954--9968}, + number = {40}, + journaltitle = {The Journal of Physical Chemistry A}, + shortjournal = {J. Phys. Chem. A}, + author = {Lienhard, Daniel M. and Bones, David L. and Zuend, Andreas and Krieger, Ulrich K. and Reid, Jonathan P. and Peter, Thomas}, + urldate = {2025-12-21}, + date = {2012-10-11}, + note = {Publisher: American Chemical Society}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/5Y4XH46R/Lienhard et al. - 2012 - Measurements of Thermodynamic and Optical Properties of Selected Aqueous Organic and Organic–Inorgan.pdf:application/pdf}, +} + +@article{lienhard_retrieving_2014, + title = {Retrieving the translational diffusion coefficient of water from experiments on single levitated aerosol droplets}, + volume = {16}, + issn = {1463-9084}, + url = {https://pubs.rsc.org/en/content/articlelanding/2014/cp/c4cp01939c}, + doi = {10.1039/C4CP01939C}, + abstract = {The time-dependent growth and shrinkage of aqueous aerosol particles trapped in an electrodynamic balance exposed to changes in relative humidity ({RH}) depend on the translational diffusion coefficient of water ({DH}2O). Resonances in the Mie scattering patterns of the illuminated micrometre-sized droplets are used to follow the compositional evolution through stepwise changes in {RH}. Under conditions where the diffusion of water molecules becomes sufficiently slow, e.g. in the highly viscous or even glassy regime, the concentration and temperature dependent values of {DH}2O can be determined iteratively by comparing the observed shifts in the Mie resonant wavelengths with predicted shifts from a diffusion model of a multi-layered sphere. It is shown that condensation and evaporation of water vapour from or to highly viscous or glassy droplets follow different kinetic regimes, a result that is consistent with previous studies of adsorption and desorption on glassy surfaces.}, + pages = {16677--16683}, + number = {31}, + journaltitle = {Physical Chemistry Chemical Physics}, + shortjournal = {Phys. Chem. Chem. Phys.}, + author = {Lienhard, Daniel M. and Huisman, Andrew J. and Bones, David L. and Te, Yiea-Funk and Luo, Bei P. and Krieger, Ulrich K. and Reid, Jonathan P.}, + urldate = {2025-12-21}, + date = {2014-07-16}, + langid = {english}, + note = {Publisher: The Royal Society of Chemistry}, + file = {Full Text PDF:/Users/davidtschan/Zotero/storage/QMD9UZ8D/Lienhard et al. - 2014 - Retrieving the translational diffusion coefficient of water from experiments on single levitated aer.pdf:application/pdf}, +} + +@article{e_jenkin_development_2000, + title = {Development and application of a possible mechanism for the generation of \textit{cis}-pinic acid from the ozonolysis of \ensuremath{\alpha}- and \ensuremath{\beta}-pinene}, + volume = {34}, + issn = {1352-2310}, + url = {https://www.sciencedirect.com/science/article/pii/S135223100000087X}, + doi = {10.1016/S1352-2310(00)00087-X}, + abstract = {Recent experimental studies have identified cis-pinic acid (a C9 dicarboxylic acid) as a condensed-phase product of the ozonolysis of both α- and β-pinene, and it is currently believed to be the most likely degradation product leading to the prompt formation of new aerosols by nucleation. The observed timescale of aerosol formation appears to require that cis-pinic acid is a first-generation product, and a possible mechanism for its formation has therefore been developed. The key step in the proposed mechanism requires that the isomerisation of a complex C9 acyl-oxy radical by a 1,7 H atom shift is able to compete with the alternative decomposition to {CO}2 and a C8 organic radical: Thermodynamic and kinetic arguments are presented, on the basis of semi-empirical electronic structure calculations, which support this proposed mechanism, and thereby the competition between the two pathways. The transfer of the labile aldehydic H atom is shown to be especially facile in this case because it occurs though an unstrained transition state; this feature can in turn be attributed to the cis-substitution of the four-membered ring, which enforces the steric proximity of the acyl-oxy and aldehyde groups. The mechanism can explain the formation of cis-pinic acid from both α- and β-pinene, because the acyl-oxy radical is likely to be formed following the decomposition of excited Criegee biradicals formed in both systems. It is also possible that a similar isomerisation reaction of a complex C10 α-carbonyl oxy radical by a 1,8 H atom shift might explain the very recently observed formation of cis-10-hydroxy-pinonic acid from α-pinene ozonolysis, and this possibility is also explored. An existing detailed scheme describing the degradation of α-pinene (part of the Master Chemical Mechanism, {MCM}) is updated to include the proposed cis-pinic acid and cis-10-hydroxy-pinonic acid formation mechanisms, and the values of several uncertain parameters are adjusted on the basis of reported yields of a series of organic products from the ozonolysis of α-pinene. The updated degradation scheme is incorporated into a boundary layer box model, and representative ambient concentrations of the organic acids and other oxygenated products are calculated for a range of representative conditions appropriate to the boundary layer over central Europe. The simulated concentrations of the organic acids in general, and cis-pinic acid in particular, are strongly dependent on the level of {NOX}, and suggest that new aerosol formation from the oxidation of α-pinene is likely to be more favoured at lower {NOX} levels.}, + pages = {2837--2850}, + number = {18}, + journaltitle = {Atmospheric Environment}, + shortjournal = {Atmospheric Environment}, + author = {E. Jenkin, Michael and Shallcross, Dudley E and Harvey, Jeremy N}, + urldate = {2025-12-21}, + date = {2000-01-01}, + keywords = {-Pinene, Acyl-oxy radicals, Carboxylic acids, Master chemical mechanism ({MCM}), Monoterpenes, Pinic acid, Secondary-organic aerosol, Tropospheric oxidation chemistry}, + file = {PDF:/Users/davidtschan/Zotero/storage/J34RL4RT/E. Jenkin et al. - 2000 - Development and application of a possible mechanism for the generation of cis-pinic acid from.pdf:application/pdf;ScienceDirect Snapshot:/Users/davidtschan/Zotero/storage/AP7475W9/S135223100000087X.html:text/html}, +} + +@article{perri_secondary_2009, + title = {Secondary organic aerosol production from aqueous photooxidation of glycolaldehyde: Laboratory experiments}, + volume = {43}, + issn = {1352-2310}, + url = {https://www.sciencedirect.com/science/article/pii/S1352231008011096}, + doi = {10.1016/j.atmosenv.2008.11.037}, + shorttitle = {Secondary organic aerosol production from aqueous photooxidation of glycolaldehyde}, + abstract = {Organic particulate matter ({PM}) formed in the atmosphere (secondary organic aerosol; {SOA}) is a substantial yet poorly understood contributor to atmospheric {PM}. Aqueous photooxidation in clouds, fogs and aerosols is a newly recognized {SOA} formation pathway. This study investigates the potential for aqueous glycolaldehyde oxidation to produce low volatility products that contribute {SOA} mass. To our knowledge, this is the first confirmation that aqueous oxidation of glycolaldehyde via the hydroxyl radical forms glyoxal and glycolic acid, as previously assumed. Subsequent reactions form formic acid, glyoxylic acid, and oxalic acid as expected. Unexpected products include malonic acid, succinic acid, and higher molecular weight compounds, including oligomers. Due to (1) the large source strength of glycolaldehyde from precursors such as isoprene and ethene, (2) its water solubility, and (3) the aqueous formation of low volatility products (organic acids and oligomers), we predict that aqueous photooxidation of glycolaldehyde and other aldehydes in cloud, fog, and aerosol water is an important source of {SOA} and that incorporation of this {SOA} formation pathway in chemical transport models will help explain the current under-prediction of organic {PM} concentrations.}, + pages = {1487--1497}, + number = {8}, + journaltitle = {Atmospheric Environment}, + shortjournal = {Atmospheric Environment}, + author = {Perri, Mark J. and Seitzinger, Sybil and Turpin, Barbara J.}, + urldate = {2025-12-21}, + date = {2009-03-01}, + keywords = {Cloud processing, Electrospray ionization mass spectrometry, Fourier transform ion cyclotron resonance mass spectrometry, Glycolaldehyde, Glycolic acid, Isoprene, Malonic acid, Oligomer, Oxalic acid, Particulate matter, Secondary organic aerosol, Succinic acid}, + file = {PDF:/Users/davidtschan/Zotero/storage/RNBJ9E28/Perri et al. - 2009 - Secondary organic aerosol production from aqueous photooxidation of glycolaldehyde Laboratory exper.pdf:application/pdf;ScienceDirect Snapshot:/Users/davidtschan/Zotero/storage/GQRTXYTA/S1352231008011096.html:text/html}, +} diff --git a/config/logos/ETH_Logo.pdf b/config/logos/ETH_Logo.pdf new file mode 100644 index 0000000..d0b8d39 Binary files /dev/null and b/config/logos/ETH_Logo.pdf differ diff --git a/config/logos/PSI_Logo.pdf b/config/logos/PSI_Logo.pdf new file mode 100644 index 0000000..e06f120 Binary files /dev/null and b/config/logos/PSI_Logo.pdf differ diff --git a/config/logos/iac_logo.pdf b/config/logos/iac_logo.pdf new file mode 100644 index 0000000..a6d100d Binary files /dev/null and b/config/logos/iac_logo.pdf differ diff --git a/config/preamble.tex b/config/preamble.tex new file mode 100644 index 0000000..e25f808 --- /dev/null +++ b/config/preamble.tex @@ -0,0 +1,421 @@ +%% ------------------------------------------------------------------% +%% LANGUAGE, FONT, SIZE, GEOMETRY ENCODINGS + +\usepackage[a4paper, + top=2cm, + bottom=2cm, + left=1.5cm, + right=1.5cm, + marginparwidth=1.75cm]{geometry} % Geometry + +\usepackage[utf8]{inputenc} +\usepackage[T1]{fontenc} +\usepackage[english]{babel} % Language +\usepackage{csquotes} % Quotation + +\usepackage{fontspec} +\usepackage{amsmath} +\usepackage{mathtools} +\usepackage[colon=literal]{unicode-math} + +% Font Selection +\setmainfont{STIX Two Text} +\setmathfont{STIX Two Math} + +\usepackage[skip=0pt, indent=15pt]{parskip} +\usepackage{enumitem} +%\setlength{\columnseprule}{0.5pt} +\setlength{\columnsep}{3em} +\setlist{leftmargin=1cm} +\renewcommand\labelitemi{--} + +%% ------------------------------------------------------------------% +%% GRAPHICS PACKAGES + +% graphics package and graphics paths +\usepackage{graphicx} +\graphicspath{{../graphics/}{../config/logos/}} + +%% ------------------------------------------------------------------% +%% PACKAGES + +%\usepackage{amsfonts} +%\usepackage{amsmath} +%\usepackage{amssymb} +\usepackage{amsthm} +\usepackage{alphalph} +\usepackage[toc,page]{appendix} +\usepackage[affil-it]{authblk} +\usepackage[backend=biber, + style=authoryear, + citestyle=authoryear, + natbib, + maxcitenames=1, + maxbibnames=99, + doi=false, + isbn=false, + url=false, + eprint=false, + giveninits=true]{biblatex} +\usepackage{blindtext} +\usepackage{commath} +%\usepackage{dblfnote} +\usepackage{dirtree} +\usepackage{dirtytalk} + +\usepackage{eso-pic} +\usepackage{epstopdf} +\epstopdfsetup{outdir=../graphics/} + +\usepackage{etoolbox} +\usepackage{fancyhdr} +\usepackage{float} +\usepackage[record=hybrid, acronym, symbols, automake, indexcrossrefs=true, autoseeindex=true, stylemods={longextra}]{glossaries-extra} +\usepackage[colorlinks=true, linktoc=true, allcolors=black]{hyperref} % allcolors=black +\usepackage{imakeidx} +\usepackage{kantlipsum} +\usepackage{lastpage} +\usepackage[switch*, modulo]{lineno} +\usepackage{mathtools} +\usepackage[arrows=pgf-filled, version=4]{mhchem} +\usepackage{multicol} +\usepackage{nameref} +\usepackage{setspace} +\usepackage[free-standing-units=true]{siunitx} +\usepackage{subcaption} +\usepackage{scrwfile} +\usepackage{tabularray} +\usepackage{tikz} +\usepackage{tikz-3dplot} +\usepackage[breakable, many]{tcolorbox} +\usepackage[titles]{tocloft} +\usepackage{verbatim} +\usepackage{xcolor} + +% Chemical equations and according setup: Needs to be loaded after \usepackage{mhchem} +\usepackage{chemmacros} +\chemsetup{ + formula=mhchem, + reactions/tag-open=[R, + reactions/tag-close=] +} + +\counterwithin{reaction}{section} + +%% ------------------------------------------------------------------% +%% TITLE FORMAT + +% Formatting author and affiliation fonts +\renewcommand\Authfont{\Large\normalfont} +\renewcommand\Affilfont{\normalsize\normalfont} + +\makeatletter +\renewcommand{\maketitle}{ + \thispagestyle{empty} + + \begin{minipage}[b]{0.3\textwidth} + \centering + \includegraphics[height=1.5cm]{ETH_Logo.pdf} + \end{minipage} + \hfill + \begin{minipage}[b]{0.3\textwidth} + \centering + \includegraphics[height=1.5cm]{iac_logo.pdf} + \end{minipage} + \hfill + \begin{minipage}[b]{0.3\textwidth} + \centering + \includegraphics[height=1.5cm]{PSI_Logo.pdf} + \end{minipage} + + \vspace*{6cm} + + \begin{flushleft} + \textsc{\@subject} + \end{flushleft} + + \vspace*{-0.25cm} + + \begin{flushleft} + \LARGE{\scshape{\@title}} + \end{flushleft} + + \vspace*{-0.25cm} + + \begin{flushleft} + \Large\textsc{\@subtitle} + \end{flushleft} + + \vfill + + \begin{flushleft} + \large\@author + \end{flushleft} + + \vspace*{0.5cm} + + \begin{flushleft} + \textnormal{Student-ID: 20-914-180}\\ + \textnormal{E-Mail: }\href{mailto:datschan@student.ethz.ch}{\small\texttt{datschan@student.ethz.ch}} + \end{flushleft} + + \vspace*{0.5cm} + + \begin{flushleft} + \normalsize\textbf{Supervised By:}\\ + + \vspace*{0.25cm} + + Prof. Dr. Markus Ammann\textsuperscript{2}\\ + Nicole Carina Leemann\textsuperscript{2}\\ + + \vspace*{0.25cm} + + \normalsize\normalfont{\textsuperscript{2}Laboratory of Atmospheric Chemistry,\linebreak{Paul Scherrer Institut PSI}} + \end{flushleft} + + \vspace*{0.5cm} + + \begin{flushleft} + \Large\@date + \end{flushleft} + + \pagebreak + +}\makeatother + +%% ------------------------------------------------------------------% +%% FORMATTING + +% Line Spacing +\renewcommand{\baselinestretch}{1.0} + +% Numbering +\makeatletter +\newcommand{\@alphalph}{} +\let\@alphalph=\alphalph +\makeatother +\allowdisplaybreaks + +% Tabularray Setup +\UseTblrLibrary{booktabs} +\DefTblrTemplate{caption-tag}{default}{\small\bfseries\scshape{Table \thetable}} +\DefTblrTemplate{caption-text}{default}{\small\InsertTblrText{caption}} +\DefTblrTemplate{caption-sep}{default}{\small\bfseries{:}\enskip} +\SetTblrStyle{foot}{font={\normalfont\small}} +\renewcommand\TblrOverlap[1]{#1} +%\setlength{\DTbaselineskip}{} +\SetTblrStyle{conthead-text}{font={\normalfont\small}} + +% Section Title Formatting +\setkomafont{chapter}{\normalfont\Large\bfseries} +\setkomafont{section}{\normalfont\large\bfseries} +\setkomafont{subsection}{\normalfont\normalsize\bfseries} +\setkomafont{subsubsection}{\normalfont\normalsize\bfseries} +\setkomafont{captionlabel}{\normalfont\small\bfseries\scshape} +\setkomafont{caption}{\normalfont\small} +\renewcaptionname{english}{\figurename}{Figure } +\renewcaptionname{english}{\tablename}{Table } +\patchcmd{\chapter}{\thispagestyle{plain}}{\thispagestyle{proposal}}{}{} + +% Formatting for TOC +\addtokomafont{chapterentry}{\normalfont\bfseries} + + +% Roman Numbers +\newcommand{\toRoman}[1]{\MakeUppercase{\romannumeral #1}} + +% SI unit and SI settings (siunitx) +\DeclareSIUnit\amu{u} +\DeclareSIUnit\bar{bar} +\DeclareSIUnit\year{yr} +\DeclareSIUnit\month{m} +\DeclareSIUnit\week{w} +\DeclareSIUnit\day{d} +\DeclareSIUnit\ppm{ppm} +\DeclareSIUnit\ppt{ppt} +\DeclareSIUnit\pptv{pptv} +\DeclareSIUnit\atm{atm} +\DeclareSIUnit\Molar{M} +\DeclareSIUnit\gramCarbon{g\ce{C}} +\DeclareSIUnit\permille{\text{\textperthousand}} +\sisetup{separate-uncertainty, multi-part-units=single, range-units=single, range-phrase=\ensuremath{\ldots}} + +% Bibliogrpahy Format +\AtBeginBibliography{\small} +\AtEveryBibitem{\clearfield{note}} + +% Header and Footer Setup +\fancypagestyle{mainbody}{ + \fancyhead[RO, LE]{D. Tschan} + \fancyhead[LO, RE]{\textit\leftmark} + \fancyfoot[RO, LE]{\thepage\text{ of }\pageref{LastPage}} + \fancyfoot[CO, CE]{} + \fancyfoot[LO, RE]{\textit\rightmark} +} + +\fancypagestyle{proposal}{ + \fancyhead[RO, LE]{D. Tschan} + \fancyhead[LO, RE]{D-USYS Master Thesis Proposal} + \fancyfoot[RO, LE]{\thepage\text{ of }\pageref{LastPage}} + \fancyfoot[CO, CE]{} + \fancyfoot[LO, RE]{\textit\leftmark} +} + +% Dirtree Setup +\newcommand\mydirtree[1]{{\ttfamily\small\dirtree{#1}\par}} + +%% ------------------------------------------------------------------% +%% GLOSSARIES SETUP + +% Create new glossary type +\newglossary*{species}{species} + +% Compile the glossaries +\makeglossaries +\makeindex[options=-s ../main/index.ist, name=main, intoc, columns=3] + +% Also adds the actual entry in the glossary to the index +\glssetcategoryattribute{main}{indexname}{textbf} +\glssetcategoryattribute{main}{dualindex}{true} + +% Formatting command... +\GlsXtrEnableIndexFormatOverride + +% Prevents character escaping +\renewcommand*{\glsxtrautoindexesc}{} + +% Sets the correct sorting in the index +\renewcommand*{\glsxtrautoindexentry}[1]{\string\glsentryuseri{#1}} +\renewcommand*{\glsxtrautoindexassignsort}[2]{% + \glsletentryfield{#1}{#2}{user1}% +} + +% Sets the correct sorting in the index +\renewcommand*{\glsxtrautoindexassignsort}[2]{% + \ifglshasshort{#2}% + {\glsletentryfield{#1}{#2}{sort}}% + {\glsletentryfield{#1}{#2}{sort}}% +} + +\indexsetup{firstpagestyle=mainbody} + +%% SYMBOLS + +% Add glossary key 'unit' and 'formula' +\glsaddkey{unit}{}{\glsentryunit}{\Glsentryunit}{\glsunit}{\Glsunit}{\GLSunit} +\glsxtrprovidestoragekey{formula}{}{\Formula} + +\GlsXtrLoadResources[ + src={../config/symbols}, % data in symbols.bib + sort-field={desc}, % sort by name field + sort={letter-nocase}, % case-insensitive letter sort + type=symbols, % put these terms in the symbols list + field-aliases={unit=symbol}, % convert unit key to symbol + save-locations=false % don't save location lists +] + +%% CHEMICAL SPECIES + +% \glsaddkey{formula}{}{\glsentryformula}{\Glsentryformula}{\glsformula}{\Glsformula}{\GLSformula} + +\GlsXtrLoadResources[ + src={../config/species}, % data in symbols.bib + sort-field={desc}, % sort by name field + sort={letter-nocase}, % case-insensitive letter sort + type=species, % put these terms in the symbols list + field-aliases={formula=symbol}, % convert unit key to symbol + save-locations=false % don't save location lists +] + + +% Enable hyperlinks for glossary +\glsenablehyper + +%% ------------------------------------------------------------------% +%% THEOREMS AND ENVIRONMENTS + +% General modifications + +\renewcommand{\qedsymbol}{\ensuremath{\blacksquare}} + +% Color definitions + +\definecolor{color_box}{HTML}{EEEEEE} +\definecolor{color_box_lower}{HTML}{DDDDDD} +\definecolor{definition_color_title}{HTML}{C63B3B} +\definecolor{example_color_title}{HTML}{005B2F} +\definecolor{theorem_color_title}{HTML}{AD4CBB} +\definecolor{law_color_title}{HTML}{4C84BB} + +% Definitions + +\newcounter{def_custom} +\newtcolorbox[use counter=def_custom, + number within=section] + {definition_custom}[2]{ + skin=bicolor, + breakable=true, + arc=0mm, + boxrule=0pt, + colback=color_box, + colframe=definition_color_title, + label={#2}, + title={\textcolor{white}{Definition~\thetcbcounter:\enskip\bfseries\itshape{#1}}}, + segmentation style={draw=none}, + colbacklower=color_box_lower +} + +% Examples + +\newcounter{example_custom} +\newtcolorbox[use counter=example_custom, +number within=section] +{example_custom}[2]{ + skin=bicolor, + breakable=true, + arc=0mm, + boxrule=0pt, + colback=color_box, + colframe=example_color_title, + label={#2}, + title={\textcolor{white}{Example~\thetcbcounter:\enskip\bfseries\itshape{#1}}}, + segmentation style={draw=none}, + colbacklower=color_box_lower +} + +% theorems + +\newcounter{theorem_custom} +\newtcolorbox[use counter=theorem_custom, +number within=section] +{theorem_custom}[2]{ + skin=bicolor, + breakable=true, + arc=0mm, + boxrule=0pt, + colback=color_box, + colframe=theorem_color_title, + label={#2}, + title={\textcolor{white}{Theorem~\thetcbcounter:\enskip\bfseries\itshape{#1}}}, + segmentation style={draw=none}, + colbacklower=color_box_lower +} + +% Law + +\newcounter{law_custom} +\newtcolorbox[use counter=law_custom, +number within=section] +{law_custom}[2]{ + skin=bicolor, + breakable=true, + arc=0mm, + boxrule=0pt, + colback=color_box, + colframe=law_color_title, + label={#2}, + title={\textcolor{white}{Law~\thetcbcounter:\enskip\bfseries\itshape{#1}}}, + segmentation style={draw=none}, + colbacklower=color_box_lower +} diff --git a/config/species.bib b/config/species.bib new file mode 100644 index 0000000..f7d7203 --- /dev/null +++ b/config/species.bib @@ -0,0 +1,481 @@ +%% DEFINE THE SPECIES TO BE USED + +% Compile via PDFLaTeX -> Bib2Gls (User) -> PDFLaTeX +% 'formula' field is accessed via \glssymbol{...} + +%% ------------------------------------------------------------------% + +@entry{I2f, + name={Molecular iodine}, + text={molecular iodine}, + formula={\ensuremath{\ce{I2}}}, + description={}, + first={molecular iodine (\ensuremath{\ce{I2}})} +} + +@entry{I-f, + name={Iodide}, + text={iodide}, + formula={\ensuremath{\ce{I-}}}, + description={}, + first={iodide (\ensuremath{\ce{I-}})} +} + +@entry{I3-f, + name={Triiodide}, + text={triiodide}, + formula={\ensuremath{\ce{I3-}}}, + description={}, + first={triiodide (\ensuremath{\ce{I3-}})} +} + +@entry{IO3-f, + name={Iodate}, + text={iodate}, + formula={\ensuremath{\ce{IO3-}}}, + description={}, + first={iodate (\ensuremath{\ce{IO3-}})} +} + +@entry{O3f, + name={Ozone}, + text={ozone}, + formula={\ensuremath{\ce{O3}}}, + description={}, + first={ozone (\ensuremath{\ce{O3}})} +} + +@entry{I.f, + name={Iodine radical}, + text={iodine radical}, + plural={iodine radicals}, + formula={\ensuremath{\ce{I}^{\bullet}}}, + description={}, + first={iodine radical (\ensuremath{\ce{I}^{\bullet}})}, + firstplural={iodine radicals (\ensuremath{\ce{I}^{\bullet}})} +} + +@entry{IO.f, + name={Iodine monoxide radical}, + text={iodine monoxide radical}, + plural={iodine monoxide radicals}, + formula={\ensuremath{\ce{IO}^{\bullet}}}, + description={}, + first={iodine monoxide radical (\ensuremath{\ce{IO}^{\bullet}})}, + firstplural={iodine monoxide radicals (\ensuremath{\ce{IO}^{\bullet}})} +} + +@entry{IO-f, + name={Iodine oxide ion}, + text={iodine oxide ion}, + formula={\ensuremath{\ce{IO-}}}, + description={}, + first={iodine oxide ion (\ensuremath{\ce{IO-}})}, + firstplural={iodine oxide ions (\ensuremath{\ce{IO-}})} +} + +@entry{IO2f, + name={Iodine dioxide}, + text={iodine dioxide}, + formula={\ensuremath{\ce{IO2}}}, + description={}, + first={iodine dioxide (\ensuremath{\ce{IO2}})}, + firstplural={iodine dioxides (\ensuremath{\ce{IO2}})} +} + +@entry{OIO.f, + name={Iodine dioxide radical}, + text={iodine dioxide radical}, + formula={\ensuremath{\ce{OIO}^{\bullet}}}, + description={}, + first={iodine dioxide radical (\ensuremath{\ce{OIO}^{\bullet}})}, + firstplural={iodine dioxide radicals (\ensuremath{\ce{OIO}^{\bullet}})} +} + +@entry{IOOO-f, + name={Iodine trioxide ion}, + text={iodine trioxide ion}, + formula={\ensuremath{\ce{IOOO-}}}, + description={}, + first={iodine trioxide ion (\ensuremath{\ce{IOOO-}})}, + firstplural={iodine trioxide ions (\ensuremath{\ce{IOOO-}})} +} + +@entry{I2O2f, + name={Diiodine dioxide}, + text={diiodine dioxide}, + formula={\ensuremath{\ce{I2O2}}}, + description={}, + first={diiodine dioxide (\ensuremath{\ce{I2O2}})}, + firstplural={diiodine dioxides (\ensuremath{\ce{I2O2}})} +} + +@entry{I2O3f, + name={Diiodine trioxide}, + text={diiodine trioxide}, + formula={\ensuremath{\ce{I2O3}}}, + description={}, + first={diiodine trioxide (\ensuremath{\ce{I2O3}})}, + firstplural={diiodine trioxides (\ensuremath{\ce{I2O3}})} +} + +@entry{I2O4f, + name={Diiodine tetroxide}, + text={diiodine tetroxide}, + formula={\ensuremath{\ce{I2O4}}}, + description={}, + first={diiodine tetrooxide (\ensuremath{\ce{I2O4}})}, + firstplural={diiodine tetroxides (\ensuremath{\ce{I2O4}})} +} + +@entry{I2O5f, + name={Diiodine pentoxide}, + text={diiodine pentoxide}, + formula={\ensuremath{\ce{I2O5}}}, + description={}, + first={diiodine pentoxide (\ensuremath{\ce{I2O5}})}, + firstplural={diiodine pentoxides (\ensuremath{\ce{I2O5}})} +} + +@entry{IClf, + name={Iodine chloride}, + text={iodine chloride}, + formula={\ensuremath{\ce{ICl}}}, + description={}, + first={iodine chloride (\ensuremath{\ce{ICl}})}, + firstplural={iodine chlorides (\ensuremath{\ce{ICl}})} +} + + +@entry{IBrf, + name={Iodine bromide}, + text={iodine bromide}, + formula={\ensuremath{\ce{IBr}}}, + description={}, + first={Iodine bromide (\ensuremath{\ce{IBr}})}, + firstplural={iodine bromides (\ensuremath{\ce{IBr}})} +} + +@entry{Br-f, + name={Bromide}, + text={bromide}, + formula={\ensuremath{\ce{Br-}}}, + description={}, + first={bromide (\ensuremath{\ce{Br-}})} +} + +@entry{IOClOf, + name={Iodine chlorine dioxide}, + text={iodine chloride dioxide}, + formula={\ensuremath{\ce{IOClO}}}, + description={}, + first={iodine chlorine dioxide (\ensuremath{\ce{IOClO}})}, + firstplural={iodine chlorine dioxides (\ensuremath{\ce{IOClO}})} +} + +@entry{IOBrOf, + name={Iodine bromine dioxide}, + text={iodine bromine dioxide}, + formula={\ensuremath{\ce{IOBrO}}}, + description={}, + first={iodine bromine dioxide (\ensuremath{\ce{IOBrO}})}, + firstplural={iodine bromine dioxides (\ensuremath{\ce{IOBrO}})} +} + +@entry{HOIf, + name={Hypoiodous acid}, + text={hypoiodous acid}, + formula={\ensuremath{\ce{HOI}}}, + description={}, + first={hypoiodous acid (\ensuremath{\ce{HOI}})}, + firstplural={hypoiodous acids (\ensuremath{\ce{HOI}})} +} + +@entry{IONO2f, + name={Iodine oxygen nitrite}, + text={iodine oxygen nitrite}, + formula={\ensuremath{\ce{IONO2}}}, + description={}, + first={iodine oxygen nitrite (\ensuremath{\ce{IONO2}})}, + firstplural={iodine oxygen nitrites (\ensuremath{\ce{IONO2}})} +} + +@entry{INO2f, + name={Iodine nitrite}, + text={iodine nitrite}, + formula={\ensuremath{\ce{INO2}}}, + description={}, + first={iodine nitrite (\ensuremath{\ce{INO2}})}, + firstplural={iodine nitrites (\ensuremath{\ce{INO2}})} +} + +@entry{CO2f, + name={Carbon dioxide}, + text={carbon dioxide}, + formula={\ensuremath{\ce{CO2}}}, + description={}, + first={carbon dioxide (\ensuremath{\ce{CO2}})}, + firstplural={carbon dioxides (\ensuremath{\ce{CO2}})} +} + +@entry{COf, + name={Carbon monoxide}, + text={carbon monoxide}, + formula={\ensuremath{\ce{CO}}}, + description={}, + first={carbon monoxide (\ensuremath{\ce{CO}})}, + firstplural={carbon monoxide (\ensuremath{\ce{CO}})} +} + +@entry{NO2f, + name={Nitrogen dioxide}, + text={nitrogen dioxide}, + formula={\ensuremath{\ce{NO2}}}, + description={}, + first={nitrogen dioxide (\ensuremath{\ce{NO2}})}, + firstplural={nitrogen dioxides (\ensuremath{\ce{NO2}})} +} + +@entry{NO3.f, + name={Nitrogen trioxide radical}, + text={nitrogen trioxide radical}, + plural={nitrogen trioxide radicals}, + formula={\ensuremath{\ce{NO3}^{\bullet}}}, + description={}, + first={nitrogen troxide radical (\ensuremath{\ce{NO3}^{\bullet}})}, + firstplural={nitrogen trioxide radical (\ensuremath{\ce{NO3}^{\bullet}})} +} + +@entry{NOf, + name={Nitrogen monoxide}, + text={nitrogen monoxide}, + formula={\ensuremath{\ce{NO}}}, + description={}, + first={nitrogen monoxide (\ensuremath{\ce{NO}})}, + firstplural={nirogen monoxides (\ensuremath{\ce{NO}})} +} + +@entry{NOxf, + name={Nitrous oxide}, + text={nitrous oxide}, + formula={\ensuremath{\ce{NO}_{x}}}, + description={Chemical family: \ensuremath{\ce{NO}_{x}\coloneqq\glssymbol{NO2f}+\glssymbol{NOf}}}, + first={nitrous oxide (\ensuremath{\ce{NO}_{x}})}, + firstplural={nitrous oxides (\ensuremath{\ce{NO}_{x}})} +} + +@entry{HO2.f, + name={Peroxide radical}, + text={peroxide radical}, + plural={peroxide radicals}, + formula={\ensuremath{\ce{HO2}^{\bullet}}}, + description={}, + first={peroxide radical (\ensuremath{\ce{HO2}^{\bullet}})}, + firstplural={peroxide radicals (\ensuremath{\ce{HO2}^{\bullet}})} +} + +@entry{HO2-f, + name={Peroxide ion}, + text={peroxide ion}, + formula={\ensuremath{\ce{HO2-}}}, + description={}, + first={peroxide ion (\ensuremath{\ce{HO2-}})}, + firstplural={peroxide ions (\ensuremath{\ce{HO2-}})} +} + +@entry{HO2.-f, + name={Peroxide ion radical}, + text={peroxide ion radical}, + plural={peroxide ion radicals}, + formula={\ensuremath{\ce{HO2}^{\bullet-}}}, + description={}, + first={peroxide ion radical (\ensuremath{\ce{HO2}^{\bullet-}})}, + firstplural={peroxide ion radicals (\ensuremath{\ce{HO2}^{\bullet-}})} +} + +@entry{OH.f, + name={Hydroxyl radical}, + text={hydroxyl radical}, + plural={hydroxyl radicals}, + sort={hydroxyl radical}, + formula={\ensuremath{\ce{HO}^{\bullet}}}, + description={}, + first={hydroxyl radical (\ensuremath{\ce{HO}^{\bullet}})}, + firstplural={hydroxyl radicals (\ensuremath{\ce{HO}^{\bullet}})} +} + +@entry{OH-f, + name={Hydroxyl ion}, + text={hydroxyl ion}, + sort={hydroxyl ion}, + formula={\ensuremath{\ce{OH-}}}, + description={}, + first={hydroxyl ion (\ensuremath{\ce{HO-}})}, + firstplural={hydroxyl ions (\ensuremath{\ce{HO-}})} +} + +@entry{HOxf, + name={Hydrogen oxide radical}, + text={hydrogen oxide radical}, + text={hydrogen oxide radical}, + formula={\ensuremath{\ce{HO}_{x}}}, + description={Chemical family: \ensuremath{\ce{HO}_{x}\coloneqq\glssymbol{HO2.f}+\glssymbol{OH.f}}}, + first={hydrogen oxide radical (\ensuremath{\ce{HO}_{x}})}, + firstplural={hydrogen oxide radicals (\ensuremath{\ce{HO}_{x}})}, + plural={hydrogen oxide radicals (\ensuremath{\ce{HO}_{x}})} +} + +@entry{H2O2f, + name={Hydrogen peroxide}, + text={hydrogen peroxide}, + formula={\ensuremath{\ce{H2O2}}}, + description={}, + first={hydrogen peroxide (\ensuremath{\ce{H2O2}})}, + firstplural={hydrogen peroxides (\ensuremath{\ce{H2O2}})} +} + +@entry{H2Of, + name={Water (dihydrogen oxide)}, + text={water}, + sort={dihydrogen oxide}, + formula={\ensuremath{\ce{H2O}}}, + description={}, + first={water (\ensuremath{\ce{H2O}})}, + firstplural={waters (\ensuremath{\ce{H2O}})} +} + +@entry{NaIO3f, + name={Sodium iodate}, + text={sodium iodate}, + formula={\ensuremath{\ce{NaIO3}}}, + description={}, + first={sodium iodate (\ensuremath{\ce{NaIO3}})} +} + +@entry{ABSf, + name={Ammonium Bisulfate}, + text={ammonium bisulfate}, + formula={\ensuremath{\ce{(NH4)HSO4}}}, + description={(ABS)}, + first={} +} + +@entry{Fe2O3f, + name={Iron(\toRoman{3}) oxide}, + text={iron(\toRoman{3}) oxide}, + formula={\ensuremath{\ce{Fe2O3}}}, + description={When occuring as a bulk crystal, this mineral is referred to as hematite.}, + first={hematite (iron(\toRoman{3}) oxide) (\ensuremath{\ce{Fe2O3}})} +} + +@entry{O2f, + name={Molecular oxygen}, + text={molecular oxygen}, + formula={\ensuremath{\ce{O2}}}, + description={}, + sort={oxygen} +} + +@entry{O2-.f, + name={Superoxide ion radical}, + text={superoxide ion radical}, + plural={superoxide ion radicals}, + formula={\ensuremath{\ce{O2}^{\bullet-}}}, + first={superoxide ion radical (\ensuremath{\ce{O2}^{\bullet-}})}, + description={} +} + +@entry{O-3P.f, + name={Oxygen radical (triplet-P)}, + text={oxygen radical (triplet-P)}, + plural={oxygen radicals (triplet-P)}, + formula={\ensuremath{^{\bullet}\ce{O}(^{3}\textnormal{P})}}, + first={oxygen radical (triplet-P)}, + description={} +} + +@entry{O-1D.f, + name={Oxygen radical (singlet-D)}, + text={oxygen radical (singlet-D)}, + plural={oxygen radicals (singlet-D)}, + formula={\ensuremath{^{\bullet}\ce{O}(^{1}D)}}, + first={oxygen radical (singlet-D) (\ensuremath{^{\bullet}\ce{O}(^{1}D)})}, + description={} +} + +@entry{H+f, + name={Hydrogen ion}, + text={hydrogen ion}, + formula={\ensuremath{\ce{H+}}}, + first={hydrogen ion (\ensuremath{\ce{H+}})}, + description={} +} + +@entry{RInf, + name={\gls{VOICa}}, + text={\gls{VOICa}}, + plural={\glspl{VOICa}}, + formula={\ensuremath{\RI{n}}}, + first={\gls{VOICa} (\ensuremath{\RI{n}})}, + firstplural={\glspl{VOICa} (\ensuremath{\RI{n}})}, + description={} +} + +@entry{CH3If, + name={Methyl iodide}, + text={methly iodide}, + formula={\ensuremath{\ce{CH3I}}}, + first={(\ensuremath{\ce{CH3I}})}, + description={} +} + +@entry{Iyf, + name={Total inorganic iodine}, + text={total inorganic iodine}, + formula={\ensuremath{\ce{I}_{y}}}, + first={total inorganic iodine (\ensuremath{\ce{I}_{y}})}, + description={Chemical family: \ensuremath{\ce{I}_{y}\coloneqq\glssymbol{I.f}+\glssymbol{IO.f}+\glssymbol{IO2f}+\glssymbol{HOIf}+\ce{HI}+\ce{INO}+\ce{INO2}+\glssymbol{IONO2f}+2\glssymbol{I2f}+\ce{ICl}+\ce{IBr}+2\ce{I2O2}+2\ce{I2O3}+2\ce{I2O4}}} +} + +@entry{Ix.f, + name={Iodine radical species}, + text={iodine radical species}, + formula={\ensuremath{\ce{I}_{x}}}, + first={iodine radical species (\ensuremath{\ce{I}_{x}})}, + description={Chemical family: \ensuremath{\ce{I}_{x}\coloneqq\glssymbol{I.f}+\glssymbol{IO.f}}} +} + +@entry{ISOPRENEf, + name={isoprene}, + text={isoprene}, + formula={\ensuremath{\ce{C5H8}}}, + first={isoprene (2-metyhl-1,3-butadiene) (\ensuremath{\ce{CH2=C(CH3)-CH=CH2}})}, + description={2-metyhl-1,3-butadiene} +} + +@entry{A-PINENEf, + name={\ensuremath{\alpha}-pinene}, + text={\ensuremath{\alpha}-pinene}, + formula={\ensuremath{\ce{C10H16}}}, + first={\ensuremath{\alpha}-pinene (2,6,6-trimethylbicyclo[3.1.1]hept-2-ene)}, + description={2,6,6-trimethylbicyclo[3.1.1]hept-2-ene. Two enantiomers exist.} +} + +@entry{B-PINENEf, + name={\ensuremath{\beta}-pinene}, + text={\ensuremath{\beta}-pinene}, + formula={\ensuremath{\ce{C10H16}}}, + first={\ensuremath{\beta}-pinene (6,6-dimethyl-2-methylidenebicyclo[3.1.1]heptane)}, + description={6,6-dimethyl-2-methylidenebicyclo[3.1.1]heptane} +} + +@entry{LIMONENEf, + name={Limonene}, + text={limonene}, + formula={\ensuremath{\ce{C10H16}}}, + first={limonene (1-methyl-4-(prop-1-en-2-yl)cyclohex-1-ene)}, + description={1-methyl-4-(prop-1-en-2-yl)cyclohex-1-ene} +} + + +%% ------------------------------------------------------------------% diff --git a/config/symbols.bib b/config/symbols.bib new file mode 100644 index 0000000..a5c3799 --- /dev/null +++ b/config/symbols.bib @@ -0,0 +1,58 @@ +%% DEFINE THE SYMBOLS TO BE USED + +% Compile via PDFLaTeX -> Bib2Gls (User) -> PDFLaTeX +% 'unit' field is accessed via \glssymbol{...} + +%% ------------------------------------------------------------------% + +@symbol{RHs, + unit={\qty{}{\percent}}, + name={\ensuremath{\varphi}}, + description={Water content of gas relative to saturation water content, a function of temperature and pressure.}, + set-widest=True +} + +% atmospheric mixing ratio +@symbol{CHIs, + unit={\qty{}{\pptv}}, + name={\ensuremath{\chi}}, + description={atmospheric mixing ratio}, +} + +@symbol{ALWs, + unit={\qty{}{\liter\per\cubic\meter}}, + name={\ensuremath{\omega_{\textnormal{ALW}}}}, + description={\Glsfirst{ALWa}: the volume of liquid water in aerosol phase per volume of air.} +} + +@symbol{TAUs, + unit={\qty{}{\second}}, + name={\ensuremath{\tau}}, + description={Chemical lifetime.} +} + +@symbol{pHs, + unit={}, + name={\ensuremath{\textnormal{pH}}}, + description={Measure of acidity of a solution: \ensuremath{\textnormal{pH}\coloneqq-\log_{10}\left[\ce{H+(aq)}\right]}} +} + +@symbol{ABS-TEMPs, + unit={\qty{}{\kelvin}}, + name={\ensuremath{\textnormal{T}}}, + description={Absolute thermodynamic temperature} +} + +@symbol{REL-TEMPs, + unit={\qty{}{\degreeCelsius}}, + name={\ensuremath{\vartheta}}, + description={Relative temperature} +} + +@symbol{LAMBDAs, + unit={\qty{}{\nano\meter}}, + name={\ensuremath{\lambda}}, + description={Wavelength} +} + +%% ------------------------------------------------------------------% diff --git a/graphics/ETH_Logo-eps-converted-to.pdf b/graphics/ETH_Logo-eps-converted-to.pdf new file mode 100644 index 0000000..a444699 Binary files /dev/null and b/graphics/ETH_Logo-eps-converted-to.pdf differ diff --git a/graphics/flowcharts/OFR_Flowchart.pdf b/graphics/flowcharts/OFR_Flowchart.pdf new file mode 100644 index 0000000..63a27f3 Binary files /dev/null and b/graphics/flowcharts/OFR_Flowchart.pdf differ diff --git a/graphics/flowcharts/OFR_for_Protocol.pdf b/graphics/flowcharts/OFR_for_Protocol.pdf new file mode 100644 index 0000000..9b53e14 Binary files /dev/null and b/graphics/flowcharts/OFR_for_Protocol.pdf differ diff --git a/graphics/flowcharts/OFR_for_Protocol.png b/graphics/flowcharts/OFR_for_Protocol.png new file mode 100644 index 0000000..d513d9d Binary files /dev/null and b/graphics/flowcharts/OFR_for_Protocol.png differ diff --git a/graphics/flowcharts/method_overview.pdf b/graphics/flowcharts/method_overview.pdf new file mode 100644 index 0000000..9214e1c Binary files /dev/null and b/graphics/flowcharts/method_overview.pdf differ diff --git a/graphics/inkscape_preamble.tex b/graphics/inkscape_preamble.tex new file mode 100644 index 0000000..c752f34 --- /dev/null +++ b/graphics/inkscape_preamble.tex @@ -0,0 +1,43 @@ +% !TeX program = lualatex + +\documentclass[10pt]{scrreprt} +\usepackage[utf8]{inputenc} +\usepackage[T1]{fontenc} +\usepackage[english]{babel} % Language +\usepackage{csquotes} % Quotation +\usepackage{fontspec} +\usepackage{amsmath} +\usepackage{accents} +\usepackage{mathtools} +\usepackage[colon=literal]{unicode-math} +\setmainfont{STIX} +\setmathfont{STIX Two Math} +\usepackage{graphicx} +\usepackage{alphalph} +\usepackage{commath} +\usepackage{mathtools} +\usepackage[arrows=pgf-filled, version=4]{mhchem} +\usepackage[free-standing-units=true]{siunitx} +\usepackage{xcolor} + +% Roman Numbers +\newcommand{\toRoman}[1]{\MakeUppercase{\romannumeral #1}} + +% SI unit and SI settings (siunitx) +\DeclareSIUnit\amu{u} +\DeclareSIUnit\bar{bar} +\DeclareSIUnit\year{yr} +\DeclareSIUnit\month{m} +\DeclareSIUnit\week{w} +\DeclareSIUnit\day{d} +\DeclareSIUnit\ppm{ppm} +\DeclareSIUnit\ppt{ppt} +\DeclareSIUnit\pptv{pptv} +\DeclareSIUnit\atm{atm} +\DeclareSIUnit\Molar{M} +\DeclareSIUnit\gramCarbon{g\ce{C}} +\DeclareSIUnit\permille{\text{\textperthousand}} +\sisetup{separate-uncertainty, multi-part-units=single, range-units=single, range-phrase=\ensuremath{\ldots}} + + +\newcommand{\der}[1]{\ensuremath{\textnormal{d}\,{#1}}} \ No newline at end of file diff --git a/graphics/processes/ozone_surface.pdf b/graphics/processes/ozone_surface.pdf new file mode 100644 index 0000000..29925d5 Binary files /dev/null and b/graphics/processes/ozone_surface.pdf differ diff --git a/graphics/processes/solution_creation.pdf b/graphics/processes/solution_creation.pdf new file mode 100644 index 0000000..35f63a2 Binary files /dev/null and b/graphics/processes/solution_creation.pdf differ diff --git a/graphics/proposal/Reza-et-al-2024-fig-5.jpeg b/graphics/proposal/Reza-et-al-2024-fig-5.jpeg new file mode 100644 index 0000000..0889dc4 Binary files /dev/null and b/graphics/proposal/Reza-et-al-2024-fig-5.jpeg differ diff --git a/graphics/title_page.pdf b/graphics/title_page.pdf new file mode 100644 index 0000000..ecb7c5c Binary files /dev/null and b/graphics/title_page.pdf differ diff --git a/graphics/title_page.png b/graphics/title_page.png new file mode 100644 index 0000000..914d859 Binary files /dev/null and b/graphics/title_page.png differ diff --git a/main/.../config/glossary.tex b/main/.../config/glossary.tex new file mode 100644 index 0000000..e69de29 diff --git a/main/index.ist b/main/index.ist new file mode 100644 index 0000000..9f935f5 --- /dev/null +++ b/main/index.ist @@ -0,0 +1,6 @@ +headings_flag 1 +heading_prefix "{\\bfseries " +heading_suffix "}\\nopagebreak\n" +delim_0 " \\dotfill " +delim_1 " \\dotfill " +delim_2 " \\dotfill " \ No newline at end of file diff --git a/main/main.glo-abr b/main/main.glo-abr new file mode 100644 index 0000000..fff568a --- /dev/null +++ b/main/main.glo-abr @@ -0,0 +1 @@ +\glossaryentry{PP?\glossentry{PP}|setentrycounter[]{page}"\glsnumberformat}{4} diff --git a/main/main.ist b/main/main.ist new file mode 100644 index 0000000..22be024 --- /dev/null +++ b/main/main.ist @@ -0,0 +1,29 @@ +% makeindex style file created by the glossaries package +% for document 'main' on 2026-8-10 +actual '?' +encap '|' +level '!' +quote '"' +keyword "\\glossaryentry" +preamble "\\glossarysection[\\glossarytoctitle]{\\glossarytitle}\\glossarypreamble\n\\begin{theglossary}\\glossaryheader\n" +postamble "\%\n\\end{theglossary}\\glossarypostamble\n" +group_skip "\\glsgroupskip\n" +item_0 "\%\n" +item_1 "\%\n" +item_2 "\%\n" +item_01 "\%\n" +item_x1 "\\relax \\glsresetentrylist\n" +item_12 "\%\n" +item_x2 "\\relax \\glsresetentrylist\n" +delim_0 "\{\\glossaryentrynumbers\{\\relax " +delim_1 "\{\\glossaryentrynumbers\{\\relax " +delim_2 "\{\\glossaryentrynumbers\{\\relax " +delim_t "\}\}" +delim_n "\\delimN " +delim_r "\\delimR " +headings_flag 1 +heading_prefix "\\glsgroupheading\{" +heading_suffix "\}\\relax \\glsresetentrylist " +symhead_positive "glssymbols" +numhead_positive "glsnumbers" +page_compositor "." diff --git a/main/main.pdf b/main/main.pdf new file mode 100644 index 0000000..c281f74 Binary files /dev/null and b/main/main.pdf differ diff --git a/main/main.tex b/main/main.tex new file mode 100644 index 0000000..7dfffd1 --- /dev/null +++ b/main/main.tex @@ -0,0 +1,191 @@ +% !TeX program = lualatex + +%% ------------------------------------------------------------------% +%% DOCUMENTS SETTINGS +\documentclass[ + 12pt, + twoside, + fleqn, + method=right]{scrreprt} + +%% PREAMBLE +\input{../config/preamble.tex} +\usepackage{subfiles} + +%% BIB RESOURCE +\addbibresource{../config/literature.bib} + +%% GLOSSARY +\input{../config/glossary} + +%% CUSTOM COMMANDS +\input{../config/commands.tex} + +%% TITLE DEFINITION + +% Add background image +\let\omaketitle\maketitle +\makeatletter +\newcommand{\mainmaketitle}{\AddToShipoutPictureBG*{\includegraphics[scale=1]{title_page.png}}\omaketitle} +\makeatother + +\author[1]{David Immanuel Tschan} +\affil[1]{Institute of Amtospheric and Climate Science,\linebreak{Department of Environmental Sciences, ETH Zürich}} + + +\subject{Master Thesis} +\title{Photochemical reduction of Iodate through + Iron-containing Complexes in Secondary Organic + Aerosol from Monoterpene Oxidation} +\subtitle{} +\date{20.05.2026 --- 02.12.2026} +\publishers{Unpublished: 1st Edition} + +\makeindex[options=-s index.ist, intoc, name=main, columns=3] +\makeglossaries +\indexsetup{firstpagestyle=mainbody} + +%% ------------------------------------------------------------------% + + +\begin{document} + + %% ------------------------------------------------------------------% + % FRONTMATTER + + \pagestyle{mainbody} + + \mainmaketitle + %\pagebreak + + \thispagestyle{empty} + \small{Title page image courtesy to \href{https://unsplash.com/@asoggetti}{Alessio Soggetti} from \href{https://unsplash.com/photos/mountains-covered-with-fogs-gdE-5Oui1Y0?utm_source=unsplash&utm_medium=referral&utm_content=creditCopyText}{unsplash.com}, accessed on 26.05.2026 10:00. + + + The font used in figures including technical drawings (figs. ...) was accessed from \href{https://github.com/hikikomori82/osifont}{https://github.com/hikikomori82/osifont} on 06.08.2026 09:25 and is distributed under the GNU GPL V3 + FE license. + + Beaker in figure \ref{methods: fig: solution preparation} was adapted from Diogo Losch De Oliveira (2026). Beakers [Illustration]. CC-BY 4.0. SciDraw.io. https://scidraw.io/drawing/beakers-ba8583ed. Accessed 10.08.2026 16:16} + \pagebreak + + \pagestyle{mainbody} + + \tableofcontents + \listoftables + \listoffigures + \clearpage + + %% ------------------------------------------------------------------% + % MAINMATTER + + \modulolinenumbers[1] + \linenumbers + \doublespacing + + \subfile{../chapters/introduction.tex} + \subfile{../chapters/methods.tex} + %\subfile{../chapters/results.tex} + %\subfile{../chapters/discussion.tex} + %\subfile{../chapters/conclusion.tex} + %\subfile{../chapters/acknowledgements.tex} + + + + + %% ------------------------------------------------------------------% + % BACKMATTER + \singlespacing + + + %% ------------------------------------------------------------------% + % BIBLIOGRAPHY + \printbibliography[heading=bibintoc] + \clearpage + + + + + %% ------------------------------------------------------------------% + % ACRONYMS + + %% Formatting for acronyms + \renewcommand{\glsnamefont}[1]{\normalfont\textbf{#1}} + + % print acronyms + \setabbreviationstyle[acronym]{long-short} + \printglossary[type=\acronymtype, style=index] + \thispagestyle{proposal} + + + + + %% ------------------------------------------------------------------% + % SYMBOLS + + % Formatting for symbols + \renewcommand{\glsnamefont}[1]{\normalfont{#1}} + + % change column headers: + \renewcommand{\entryname}{Symbol} + \renewcommand{\symbolname}{Unit} + + % Adjusts the column widths for the symbols list + \setlength{\tabcolsep}{5pt} + \renewcommand{\glslongextraDescAlign}{>{\raggedright\arraybackslash}p{\dimexpr 0.7\textwidth - \tabcolsep - \tabcolsep}} % Description + \renewcommand{\glslongextraNameAlign}{>{\raggedright\arraybackslash}p{\dimexpr 0.12\textwidth - \tabcolsep - \tabcolsep}} % Symbol + \renewcommand{\glslongextraSymbolAlign}{>{\raggedright\arraybackslash}p{\dimexpr 0.18\textwidth - \tabcolsep - \tabcolsep}} % Unit + + % print list of symbols + \renewcommand{\arraystretch}{0.6} + \printunsrtglossary[type=symbols, style=long-name-desc-sym, title={List of Symbols}, toctitle={List of Symbols}] + \thispagestyle{proposal} + + + + + %% ------------------------------------------------------------------% + % CHEMICAL SPECIES + + % Formatting for chemical species + \renewcommand{\glsnamefont}[1]{\normalfont{#1}} + + % change column headers: + \renewcommand{\entryname}{Name} + \renewcommand{\symbolname}{Formula} + \renewcommand{\descriptionname}{Comment} + + % Adjusts the column widths for the symbols list + \setlength{\tabcolsep}{5pt} + \renewcommand{\glslongextraDescAlign}{>{\raggedright\arraybackslash}p{\dimexpr 0.5\textwidth - \tabcolsep - \tabcolsep}} % Description + \renewcommand{\glslongextraNameAlign}{>{\raggedright\arraybackslash}p{\dimexpr 0.25\textwidth - \tabcolsep - \tabcolsep}} % Name + \renewcommand{\glslongextraSymbolAlign}{>{\raggedright\arraybackslash}p{\dimexpr 0.25\textwidth - \tabcolsep - \tabcolsep}} % Fomula + + % print list of speces + \renewcommand{\arraystretch}{1.1} + \printunsrtglossary[type=species, style=long-name-desc-sym, title={List of Species}, toctitle={List of Species}] + \thispagestyle{proposal} + + + + + %% ------------------------------------------------------------------% + % GLOSSARY + + % Formatting for symbols + \renewcommand{\glsnamefont}[1]{\normalfont\bfseries{#1}} + + \printglossary[type=main, toctitle=Glossary, style=index] + \thispagestyle{proposal} + + + + + %% ------------------------------------------------------------------% + % INDEX + + % Formatting for index + \renewcommand{\glsnamefont}[1]{\normalfont\bfseries{#1}} + + \printindex + \thispagestyle{mainbody} + +\end{document} \ No newline at end of file