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1. Chemical Speciation: Defining the Niche of Hot Spring Ammonia-Oxidizing Archaea (Oral Presentation)

   Weeks, Katelyn; Trembath-Reichert, Elizabeth; Robare, Jordyn; Debes, Vincent R; Howells, Alta; Boyer, Grayson; Shock, Everett L (July 2025, Goldschmidt 2025 Conference)

   The availability of chemical energy supplies is fundamental to environmental and planetary habitability. However, the presence of a chemical energy supply does not guarantee the presence of microorganisms capable of consuming it. In this study, chemical energy supplies available in Yellowstone National Park (YNP) hot springs were calculated, and the results indicate that ammonia oxidation, calculated using total dissolved ammonia, is one of the major energy supplies. Nevertheless, known ammonia-oxidizers (AO) are only present in a small fraction of the hot springs tested. Where AO are present, they do not dominate the microbial communities (relative abundances <5%), even in cases where total dissolved ammonia oxidation is the richest energy supply. The AO in YNP hot springs are predominantly ammonia-oxidizing archaea (AOA), which tend to favor environments with low total ammonia (sum of NH3 and NH4+) concentrations, despite the requirement of ammonia (NH3) as a substrate. Hot spring pH and temperature determine the ratio of NH3 to NH4+ and, consequently, NH3 availability to resident AOA. In this study, total ammonia measurements were collected from YNP hot spring samples using ion chromatography in coordination with biological sampling. DNA was extracted from simultaneously collected samples for 16S rRNA gene sequencing and analysis, and for the identification of known AOA. The WORM-portal (https://worm-portal.asu.edu/) was used to speciate the total ammonia measurements into ammonia and ammonium activities. By performing speciation calculations, we identified a potential lower limit for substrate (NH3) availability and a potential upper limit for NH4+ concentrations for the YNP hot spring AOA. Thus, the niche for AOA across YNP hot springs is dictated by the form of the total dissolved ammonia present, not by the energy supply available for total dissolved ammonia oxidation. 

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2. Ab Initio Calculations on the Ground and Excited Electronic States of Thorium–Ammonia, Thorium–Aza-Crown, and Thorium–Crown Ether Complexes

   https://doi.org/10.3390/molecules28124712  

   Lu, Zhongyuan; Jackson, Benjamin A; Miliordos, Evangelos (June 2023, Molecules)

   Positively charged metal–ammonia complexes are known to host peripheral, diffuse electrons around their molecular skeleton. The resulting neutral species form materials known as expanded or liquid metals. Alkali, alkaline earth, and transition metals have been investigated previously in experimental and theoretical studies of both the gas and condensed phase. This work is the first ab initio exploration of an f-block metal–ammonia complex. The ground and excited states are calculated for Th0–3+ complexes with ammonia, crown ethers, and aza-crown ethers. For Th3+ complexes, the one valence electron Th populates the metal’s 6d or 7f orbitals. For Th0–2+, the additional electrons prefer occupation of the outer s- and p-type orbitals of the complex, except Th(NH3)10, which uniquely places all four electrons in outer orbitals of the complex. Although thorium coordinates up to ten ammonia ligands, octa-coordinated complexes are more stable. Crown ether complexes have a similar electronic spectrum to ammonia complexes, but excitations of electrons in the outer orbitals of the complex are higher in energy. Aza-crown ethers disfavor the orbitals perpendicular to the crowns, attributed to the N-H bonds pointing along the plane of the crowns. 

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3. The impact of ammonia on particle formation in the Asian Tropopause Aerosol Layer

   https://doi.org/10.1038/s41612-024-00758-3  

   Xenofontos, Christos; Kohl, Matthias; Ruhl, Samuel; Almeida, João; Beckmann, Hannah M; Caudillo-Plath, Lucía; Ehrhart, Sebastian; Höhler, Kristina; Kaniyodical_Sebastian, Milin; Kong, Weimeng; et al (December 2024, npj Climate and Atmospheric Science)

   Abstract During summer, ammonia emissions in Southeast Asia influence air pollution and cloud formation. Convective transport by the South Asian monsoon carries these pollutant air masses into the upper troposphere and lower stratosphere (UTLS), where they accumulate under anticyclonic flow conditions. This air mass accumulation is thought to contribute to particle formation and the development of the Asian Tropopause Aerosol Layer (ATAL). Despite the known influence of ammonia and particulate ammonium on air pollution, a comprehensive understanding of the ATAL is lacking. In this modelling study, the influence of ammonia on particle formation is assessed with emphasis on the ATAL. We use the EMAC chemistry-climate model, incorporating new particle formation parameterisations derived from experiments at the CERN CLOUD chamber. Our diurnal cycle analysis confirms that new particle formation mainly occurs during daylight, with a 10-fold enhancement in rate. This increase is prominent in the South Asian monsoon UTLS, where deep convection introduces high ammonia levels from the boundary layer, compared to a baseline scenario without ammonia. Our model simulations reveal that this ammonia-driven particle formation and growth contributes to an increase of up to 80% in cloud condensation nuclei (CCN) concentrations at cloud-forming heights in the South Asian monsoon region. We find that ammonia profoundly influences the aerosol mass and composition in the ATAL through particle growth, as indicated by an order of magnitude increase in nitrate levels linked to ammonia emissions. However, the effect of ammonia-driven new particle formation on aerosol mass in the ATAL is relatively small. Ammonia emissions enhance the regional aerosol optical depth (AOD) for shortwave solar radiation by up to 70%. We conclude that ammonia has a pronounced effect on the ATAL development, composition, the regional AOD, and CCN concentrations. 

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4. Urban aerosol chemistry at a land-water transition site during summer – Part 1: Impact of agricultural and industrial ammonia emissions

   Balasus, N. (January 2021, Atmospheric chemistry and physics discussion)

   null (Ed.)

   This study characterizes the impact of the Chesapeake Bay and associated meteorological phenomena on aerosol chemistry during the second Ozone Water-Land Environmental Transition Study (OWLETS-2) field campaign during summer 2018. Measurements of inorganic PM2.5 composition, gas-phase ammonia (NH3), and an array of meteorological parameters were undertaken at Hart-Miller Island (HMI), a land-water transition site just east of downtown Baltimore on the Chesapeake Bay. The observations at HMI were characterized by abnormally high NH3 concentrations (maximum of 19.3 μg m-3, average of 3.83 μg m-3), which were more than a factor of three higher than NH3 levels measured at the closest Atmospheric Ammonia Network (AMoN) site (approximately 45 km away). While sulfate concentrations at HMI agreed quite well with those measured at a regulatory monitoring station 45 km away, aerosol ammonium and nitrate concentrations were significantly higher, due to the ammonia-rich conditions that resulted from the elevated NH3. The high NH3 concentrations were largely due to regional agricultural emissions, including dairy farms in southeastern Pennsylvania and poultry operations in the Delmarva Peninsula (Delaware-Maryland-Virginia). Reduced NH3 deposition during transport over the Chesapeake Bay likely contributed to enhanced concentrations at HMI compared to the more inland AMoN site. Several peak NH3 events were recorded, including the maximum NH3 observed during OWLETS-2, that appear to originate from a cluster of industrial sources near downtown Baltimore. Such events were all associated with nighttime emissions and advection to HMI under low 15 wind speeds (< 1 m s-1) and stable atmospheric conditions. Our results demonstrate the importance of industrial sources, including several that are not represented in the emissions inventory, on urban air quality. Together with our companion paper, which examines aerosol liquid water and pH during OWLETS-2, we highlight unique processes affecting urban air quality of coastal cities that are distinct from continental locations. 

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5. On the Chlorobenzene-Ammonia Cluster Reaction: Entrance Channel Dynamics, 2CR2PI Spectroscopy, and Ion Imaging of the Reaction Dynamics

   https://doi.org/10.1021/acs.jpca.5c02264  

   Mutete, Ronald; Kokkin, Damian; Fessahaye, Natan; Howell, Thomas R; Loomis, Richard A; Reid, Scott A (September 2025, The Journal of Physical Chemistry A)

   Prior studies of halobenzene−ammonia complexes have shown that the nature of the cationic intermediate (i.e., Wheland-type vs ion-radical) may play a key role in determining the reaction products. To probe this link, we report here the reaction dynamics of the chlorobenzene-ammonia 1:1 complex (PhCl···NH3) using product ion imaging following two-color resonant two-photon ionization. A threshold value of 8.863 ± 0.008 eV was determined for the appearance of protonated aniline, which accompanies Cl atom loss and is the dominant product channel at energies near threshold. Scanning down to energies close to threshold, we find no evidence for a roaming halogen radical mechanism leading to HCl products, which was evidenced in the related bromobenzene−ammonia complex, and proceeded through an ion-radical intermediate structure. Here, supporting calculations indicate that both types of intermediates are present, but the Wheland-type structure is significantly more stable. Addressing a key question of earlier work, analysis of the PhCl···NH3 potential energy surface (PES) in the reactant region establishes a complicated entrance channel pathway linking the in-plane σ-type complex to the Wheland intermediate (iWH) on the [PhCl···NH3]+• cationic surface. This pathway involves stepwise transition of the weakly bound ammonia from the initial in-plane σ-type complex to an ortho Wheland intermediate, followed by rearrangement to the ipso position. Finally, given that fluorine has been shown to stabilize aromatic ions, we hypothesized that fluorine substitution might alter the structure of the intermediate, favoring the ion-radical intermediate. To test this hypothesis, as an illustrative example the PES of the meta-PhClF-NH3 system on the cationic surface was computed. Confirming our hypothesis, these calculations show an inversion in stability for the Wheland-type and ion−radical complex intermediates, with the latter preferred energetically at the examined level of theory. 

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