Perspective on Mechanism Development and Structure-Activity Relationships for Gas-Phase Atmospheric Chemistry

Perspective on Theoretical and Experimental Advances in Atmospheric Photochemistry

Research that explores the chemistry of Earth's atmosphere is central to the current understanding of global challenges such as climate change, stratospheric ozone depletion, and poor air quality in urban areas. This research is a synergistic combination of three established domains: earth observation, for example, using satellites, and in situ field measurements; computer modeling of the atmosphere and its chemistry; and laboratory measurements of the properties and reactivity of gas-phase molecules and aerosol particles. The complexity of the interconnected chemical and photochemical reactions which determine the composition of the atmosphere challenges the capacity of laboratory studies to provide the spectroscopic, photochemical, and kinetic data required for computer models. Here, we consider whether predictions from computational chemistry using modern electronic structure theory and nonadiabatic dynamics simulations are becoming sufficiently accurate to supplement quantitative laboratory data for wavelength-dependent absorption cross-sections, photochemical quantum yields, and reaction rate coefficients. Drawing on presentations and discussions from the CECAM workshop on Theoretical and Experimental Advances in Atmospheric Photochemistry held in March 2024, we describe key concepts in the theory of photochemistry, survey the state-of-the-art in computational photochemistry methods, and compare their capabilities with modern experimental laboratory techniques. From such considerations, we offer a perspective on the scope of computational (photo)chemistry methods based on rigorous electronic structure theory to become a fourth core domain of research in atmospheric chemistry.

Towards automated inclusion of autoxidation chemistry in models: from precursors to atmospheric implications

In the last few decades, atmospheric formation of secondary organic aerosols (SOA) has gained increasing attention due to their impact on air quality and climate. However, methods to predict their abundance are mainly empirical and may fail under real atmospheric conditions. In this work, a close-to-mechanistic approach allowing SOA quantification is presented, with a focus on a chain-like chemical reaction called "autoxidation". A novel framework is employed to (a) describe the gas-phase chemistry, (b) predict the products' molecular structures and (c) explore the contribution of autoxidation chemistry on SOA formation under various conditions. As a proof of concept, the method is applied to benzene, an important anthropogenic SOA precursor. Our results suggest autoxidation to explain up to 100% of the benzene-SOA formed under low-NO x laboratory conditions. Under atmospheric-like day-time conditions, the calculated benzene-aerosol mass continuously forms, as expected based on prior work. Additionally, a prompt increase, driven by the NO3 radical, is predicted by the model at dawn. This increase has not yet been explored experimentally and stresses the potential for atmospheric SOA formation via secondary oxidation of benzene by O3 and NO3.

Molecular Simulation for Atmospheric Reactions: Non-Equilibrium Dynamics, Roaming, and Glycolaldehyde Formation following Photoinduced Decomposition of syn-Acetaldehyde Oxide

The decomposition dynamics of vibrationally excited syn-CH3CHOO to form vinoxy + hydroxyl (CH2CHO + OH) radicals or to recombine to form glycolaldehyde (CH2OHCHO) are characterized using statistically significant numbers of molecular dynamics simulations using a full-dimensional neural-network-based potential energy surface at the CASPT2 level of theory. The computed final OH-translational and rotational state distributions agree well with experiments and probe the still unknown O-O bond strength DeOO for which best values from 22 to 25 kcal/mol are found. OH-elimination rates are consistent with experiments and do not vary appreciably with DeOO due to the non-equilibrium nature of the process. In addition to the OH-elimination pathway, OH roaming is observed following O-O scission, which leads to glycolaldehyde formation on the picosecond time scale. Together with recent work involving the methyl-ethyl-substituted Criegee intermediate, we conclude that OH roaming is a general pathway to be included in molecular-level modeling of atmospheric processes. This work demonstrates that atomistic simulations with machine-learned energy functions provide a viable route for exploring the chemistry and reaction dynamics of atmospheric reactions.

Environmental and human health impacts of volatile organic compounds: A perspective review

Volatile organic compounds (VOCs) are synthetic chemicals that are broadly used in the production of numerous day-to-day products for residential and commercial-based applications. VOCs are naturally occurring in the environment; however, average annual emissions of man-made volatile organic compounds may have increased dramatically in recent decades. Although many factors were attributed to influencing volatile compounds' emission, only mankind's activities are mainly proclaimed. Since vehicle and industrial pollution are mounting for years and years, urban areas are highly prone to the impacts of VOCs. Generally, volatile compounds are highly spontaneous and readily react with the particles of ambiance and produce a polluted atmosphere through several physical and chemical reactions. Though the volatile compounds play an indispensable role in the manufacture and maintaining the stability of many products, the health impacts associated with their prolonged exposure are gaining attention as recent research reports underline the influence of a wide range of diseases and disorders. Likewise, since the modern way of life applies a lot of day-to-day chemicals, it is imperative to spread a wide knowledge and safety aspects about these chemicals so that people of a wide category can implement preventive measures according to their exposure and living style. In this context, the review article attempts to shed light on past and current updates concerning the relationship between VOCs exposure and environmental and human health impacts.

Transfer Learning Approach to Multitarget Temperature-Dependent Reaction Rate Prediction

Accurate prediction of temperature-dependent reaction rate constants of organic compounds is of great importance to both atmospheric chemistry and combustion science. Extensive work has been done on developing automated mechanism generation systems but the lack of quality reaction rate data remains a huge bottleneck in the application of highly detailed mechanisms. Machine learning prediction models have been recently adopted to alleviate the data gap in thermochemistry and have great potential to do the same for kinetic data with the recent release of quality reaction rate data compilations. The ultimate goal is to formulate easily accessible, general-purpose, temperature-dependent, and multitarget models for the prediction of reaction rates. To that end, we propose a model that depends on the well-known Morgan fingerprints as well as learned representations transferred from the QM9 data set. We propose the use of an Arrhenius-based loss where predictions of the three modified-Arrhenius parameters (A, n, and B = E_a/R) are given instead of the direct prediction of reaction rate constants. Our model is >35% more accurate compared to a baseline model of feed forward network (FFN) on Morgan fingerprints.

CH2 + O2: reaction mechanism, biradical and zwitterionic character, and formation of CH2OO, the simplest Criegee intermediate

The singlet and triplet potential surfaces for the title reaction were investigated using the CBS-QB3 level of theory. The wave functions for some species exhibited multireference character and required the CASPT2/6-31+G(d,p) and CASPT2/aug-cc-pVTZ levels of theory to obtain accurate relative energies. A Natural Bond Orbital Analysis showed that triplet ³CH₂OO (the simplest Criegee intermediate) and ³CH₂O₂ (dioxirane) have mostly polar biradical character, while singlet ¹CH₂OO has some zwitterionic character and a planar structure. Canonical variational transition state theory (CVTST) and master equation simulations were used to analyze the reaction system. CVTST predicts that the rate constant for reaction of ¹CH₂ + ³O₂ is more than ten times as fast as the reaction of ³CH₂ (X³B₁) + ³O₂ and the ratio remains almost independent of temperature from 900 K to 3000 K. The master equation simulations predict that at low pressures the ¹CH₂O + ³O product set is dominant at all temperatures and the primary yield of OH radicals is negligible below 600 K, due to competition with other primary reactions in this complex system.

Unimolecular and water reactions of oxygenated and unsaturated Criegee intermediates under atmospheric conditions

Ozonolysis of unsaturated hydrocarbons (VOCs) is one of the main oxidation processes in the atmosphere. The stabilized Criegee intermediates (SCI) formed are highly reactive oxygenated species that potentially influence the...

Chemistry of Functionalized Reactive Organic Intermediates in the Earth's Atmosphere: Impact, Challenges, and Progress

The gas-phase oxidation of organic compounds is an important chemical process in the Earth's atmosphere. It governs oxidant levels and controls the production of key secondary pollutants, and hence has major implications for air quality and climate. Organic oxidation is largely controlled by the chemistry of a few reactive intermediates, namely, alkyl (R) radicals, alkoxy (RO) radicals, peroxy (RO₂) radicals, and carbonyl oxides (R₁R₂COO), which may undergo a number of unimolecular and bimolecular reactions. Our understanding of these intermediates, and the reaction pathways available to them, is based largely on studies of unfunctionalized intermediates, formed in the first steps of hydrocarbon oxidation. However, it has become increasingly clear that intermediates with functional groups, which are generally formed later in the oxidation process, can exhibit fundamentally different reactivity than unfunctionalized ones. In this Perspective, we explore the unique chemistry available to functionalized organic intermediates in the Earth's atmosphere. After a brief review of the canonical chemistry available to unfunctionalized intermediates, we discuss how the addition of functional groups can introduce new reactions, either by changing the energetics or kinetics of a given reaction or by opening up new chemical pathways. We then provide examples of atmospheric reaction classes that are available only to functionalized intermediates. Some of these, such as unimolecular H-shift reactions of RO₂ radicals, have been elucidated only relatively recently, and can have important impacts on atmospheric chemistry (e.g., on radical cycling or organic aerosol formation); it seems likely that other, as-yet undiscovered reactions of (multi)functional intermediates may also exist. We discuss the challenges associated with the study of the chemistry of such intermediates and review novel experimental and theoretical approaches that have recently provided (or hold promise for providing) new insights into their atmospheric chemistry. The continued use and development of such techniques and the close collaboration between experimentalists and theoreticians are necessary for a complete, detailed understanding of the chemistry of functionalized intermediates and their impact on major atmospheric chemical processes.

Screening for New Pathways in Atmospheric Oxidation Chemistry with Automated Mechanism Generation

In the Earth's atmosphere, reactive organic carbon undergoes oxidation via a highly complex, multigeneration process, with implications for air quality and climate. Decades of experimental and theoretical studies, primarily on the reactions of hydrocarbons, have led to a canonical understanding of how gas-phase oxidation of organic compounds takes place. Recent research has brought to light a number of examples where the presence of certain functional groups opens up reaction pathways for key radical intermediates, including alkyl radicals, alkoxy radicals, and peroxy radicals, that are substantially different from traditional oxidation mechanisms. These discoveries highlight the need for methods that systematically explore the chemistry of complex, functionalized molecules without being prohibitively expensive. In this work, automated reaction network generation is used as a screening tool for new pathways in atmospheric oxidation chemistry. The reaction mechanism generator (RMG) is used to generate reaction networks for the OH-initiated oxidation of 200 mono- and bifunctionally substituted n-pentanes. The resulting networks are then filtered to highlight the reactions of key radical intermediates that are fast enough to compete with traditional atmospheric removal processes as well as "uncanonical" processes which differ from traditionally accepted oxidation mechanisms. Several recently reported, uncanonical atmospheric mechanisms appear in the RMG dataset. These "proof of concept" results provide confidence in this approach as a tool in the search for overlooked atmospheric oxidation chemistry. Several previously unreported reaction types are also encountered in the dataset. The most potentially atmospherically important of these is a radical-carbonyl ring-closure reaction that produces a highly functionalized cyclic alkoxy radical. This pathway is proposed as a promising target for further study via experiments and more detailed theoretical calculations. The approach presented herein represents a new way to efficiently explore atmospheric chemical space and unearth overlooked reaction steps in atmospheric oxidation.

Kinetic Analysis of Unimolecular Reactions Following the Addition of the Hydroxyl Radical to 1,1,2-Trifluoroethene

Fluorinated olefins are valued chemicals in industry, especially as heat transfer fluids in refrigeration applications. As these volatile compounds are widely used, they may be released into the atmosphere, and investigation of their reactions in the atmosphere are therefore of importance. The kinetic analysis of the reaction mechanisms of trifluoroethene (CF₂═CHF) with hydroxyl radicals is studied using computational chemistry at the M06-2X level with the 6-311++G(2d,d,p) and aug-cc-pVDZ basis sets as well as the composite CBS-QB3 method. Rate coefficients for the proposed mechanisms are calculated using transition state theory (TST) with tunneling corrections. The calculated rate constants for OH addition to CF₂═CHF are in excellent agreement with experimental values. Kinetic parameters as a function of temperature and pressure are evaluated for the chemically activated formation and unimolecular dissociation of hydroxylfluoroalkyl intermediates. Important forward reactions result in adduct stabilization, H atoms, hydrogen fluoride (HF) via molecular elimination, and formation of fluorinated carbonyl radicals with CF₂(═O) and CHF(═O) product channels. Stabilization of initial adducts along with HF elimination are important reaction pathways under high pressure and low temperatures. Important HF eliminations and H atom transfers primarily involve H atoms from the hydroxyl group, as the C-H bonds on or adjacent to carbons with F atoms are stronger and show high barriers to H atom transfer.

Machine Learning for Chemical Reactions

Machine learning (ML) techniques applied to chemical reactions have a long history. The present contribution discusses applications ranging from small molecule reaction dynamics to computational platforms for reaction planning. ML-based techniques can be particularly relevant for problems involving both computation and experiments. For one, Bayesian inference is a powerful approach to develop models consistent with knowledge from experiments. Second, ML-based methods can also be used to handle problems that are formally intractable using conventional approaches, such as exhaustive characterization of state-to-state information in reactive collisions. Finally, the explicit simulation of reactive networks as they occur in combustion has become possible using machine-learned neural network potentials. This review provides an overview of the questions that can and have been addressed using machine learning techniques, and an outlook discusses challenges in this diverse and stimulating field. It is concluded that ML applied to chemistry problems as practiced and conceived today has the potential to transform the way with which the field approaches problems involving chemical reactions, in both research and academic teaching.

Simplified Protocol for the Calculation of Multiconformer Transition State Theory Rate Constants Applied to Tropospheric OH-Initiated Oxidation Reactions

Chemical kinetics plays a fundamental role in the understanding and modeling of tropospheric chemical processes, one of the most important being the atmospheric degradation of volatile organic compounds. These potentially harmful molecules are emitted into the troposphere by natural and anthropogenic sources and are chemically removed by undergoing oxidation processes, most frequently initiated by reaction with OH radicals, the atmosphere's "detergent". Obtaining the respective rate constants is therefore of critical importance, with calculations based on transition state theory (TST) often being the preferred choice. However, for molecules with rich conformational variety, a single-conformer method such as lowest-conformer TST is unsuitable while state-of-the-art TST-based methodologies easily become unmanageable. In this Feature Article, the author reviews his own cost-effective protocol for the calculation of bimolecular rate constants of OH-initiated reactions in the high-pressure limit based on multiconformer transition state theory. The protocol, which is easily extendable to other oxidation reactions involving saturated organic molecules, is based on a variety of freeware and open-source software and tested against a series of oxidation reactions of hydrofluoropolyethers, computationally very challenging molecules with potential environmental relevance. The main features, advantages and disadvantages of the protocol are presented, along with an assessment of its predictive utility based on a comparison with experimental rate constants.

Theoretical and experimental study of peroxy and alkoxy radicals in the NO3-initiated oxidation of isoprene

Under atmospheric conditions, nitrate-RO₂ radicals are equilibrated and react predominantly with HO₂, RO₂ and NO. The nitrate-RO chemistry is affected strongly by ring closure to epoxy radicals, impeding formation of MVK/MACR.

Experimental and theoretical study on the impact of a nitrate group on the chemistry of alkoxy radicals

The chemistry of nitrated alkoxy radicals, and its impact on RO₂ measurements using the laser induced fluorescence (LIF) technique, is examined by a combined theoretical and experimental study.

Reactants, products, and transition states of elementary chemical reactions based on quantum chemistry

Reaction times, activation energies, branching ratios, yields, and many other quantitative attributes are important for precise organic syntheses and generating detailed reaction mechanisms. Often, it would be useful to be able to classify proposed reactions as fast or slow. However, quantitative chemical reaction data, especially for atom-mapped reactions, are difficult to find in existing databases. Therefore, we used automated potential energy surface exploration to generate 12,000 organic reactions involving H, C, N, and O atoms calculated at the ωB97X-D3/def2-TZVP quantum chemistry level. We report the results of geometry optimizations and frequency calculations for reactants, products, and transition states of all reactions. Additionally, we extracted atom-mapped reaction SMILES, activation energies, and enthalpies of reaction. We believe that this data will accelerate progress in automated methods for organic synthesis and reaction mechanism generation—for example, by enabling the development of novel machine learning models for quantitative reaction prediction.

Measurement(s)	activation energy • Standard Transformed Enthalpy Change • transition state • reactant • reaction product • chemical reaction • SMILES string
Technology Type(s)	quantum chemistry computational method

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12047193

Reactivity of α,ω-Dihydrofluoropolyethers toward OH Predicted by Multiconformer Transition State Theory and the Interacting Quantum Atoms Approach

We report rate constants for the tropospheric reaction between the OH radical and α,ω-dihydrofluoropolyethers, which represent a specific class of the hydrofluoropolyethers family with the formula HF₂C(OCF₂CF₂)_p(OCF₂)_qOCF₂H. Four cases were considered: p0q2, p0q3, p1q0, and p1q1 (pxqy denoting p = x and q = y) with the calculations performed by a cost-effective protocol developed for bimolecular hydrogen-abstraction reactions. This protocol is based on multiconformer transition state theory and relies on computationally accessible M08-HX/apcseg-2//M08-HX/pcseg-1 calculations. Within the protocol's approximations, the results show that (1) the calculated rate constants are within a factor of five of the experimental results (p1q0 and p1q1) and (2) the chain length and composition have a negligible effect on the rate constants, which is consistent with the experimental work. The interacting quantum atoms energy decomposition scheme is used to analyze the observed trends and extract chemical information related to the imaginary frequencies and barrier heights that are key parameters controlling the reactivity of the reaction. The intramolecular exchange-correlation contributions in the reactants and transition states were found to be the dominating factor.

The Exploration of Chemical Reaction Networks

Modern computational chemistry has reached a stage at which massive exploration into chemical reaction space with unprecedented resolution with respect to the number of potentially relevant molecular structures has become possible. Various algorithmic advances have shown that such structural screenings must and can be automated and routinely carried out. This will replace the standard approach of manually studying a selected and restricted number of molecular structures for a chemical mechanism. The complexity of the task has led to many different approaches. However, all of them address the same general target, namely to produce a complete atomistic picture of the kinetics of a chemical process. It is the purpose of this overview to categorize the problems that should be targeted and to identify the principal components and challenges of automated exploration machines so that the various existing approaches and future developments can be compared based on well-defined conceptual principles.

A perspective on the development of gas-phase chemical mechanisms for Eulerian air quality models

An essential component of a three-dimensional air quality model is its gas-phase mechanism. We present an overview of the necessary atmospheric chemistry and a discussion of the types of mechanisms with some specific examples such as the Master Chemical Mechanism, the Carbon Bond, SAPRC and the Regional Atmospheric Chemistry Mechanism (RACM). The first versions of the Carbon Bond and SAPRC mechanisms were developed through a hierarchy of chemical species approach that relied heavily on chemical environmental chamber data. Now a new approach has been proposed where the first step is to develop a highly detailed explicit mechanism such as the Master Chemical Mechanism and the second step is to test the detailed explicit mechanism against laboratory and field data. Finally, the detailed mechanism is condensed for use in a three-dimensional air quality model. Here it is argued that the development of highly detailed explicit mechanisms is very valuable for research, but we suggest that combining the hierarchy of chemical species and the detailed explicit mechanism approaches would be better than either alone.Implication: Many gas-phase mechanisms are available for urban, regional and global air quality modeling. A "hierarchy of chemical species approach," relying heavily on smog-chamber data was used for the development of the early series of mechanisms. Now the development of large, explicit master mechanisms that may be condensed is a significant, trend. However, a continuing problem with air quality mechanism development is due to the high complexity of atmospheric chemistry and the current availability of laboratory measurements. This problem requires a balance between completeness and speculation so that models maintain their utility for policymakers.

Understanding the Impact of Relative Humidity and Coexisting Soluble Iron on the OH-Initiated Heterogeneous Oxidation of Organophosphate Flame Retardants

The current uncertainties in the reactivity and atmospheric persistence of particle-associated chemicals present a challenge for the prediction of long-range transport and deposition of emerging chemicals such as organophosphate flame retardants, which are ubiquitous in the global environment. Here, the OH-initiated heterogeneous oxidation kinetics of organophosphate flame retardants (OPFRs) coated on inert (NH₄)₂SO₄ and redox-active FeSO₄ particles were systematically determined as a function of relative humidity (RH). The derived reaction rate constants for the heterogeneous loss of tricresyl phosphate (TCP; k_TCP) and tris(2-butoxyethyl) phosphate (TBEP; k_TBEP) were in the range of (2.69-3.57) × 10^-12 and (3.06-5.55) × 10^-12 cm³ molecules^-1 s^-1, respectively, depending on the RH and coexisting Fe(II) content. The k_TCP (coated on (NH₄)₂SO₄) was relatively constant over the investigated RH range while k_TBEP was enhanced by up to 19% with increasing RH. For both OPFRs, the presence of Fe(II) enhanced their k by up to 53% over inert (NH₄)₂SO₄. These enhancement effects (RH and Fe(II)) were attributed to fundamental changes in the organic phase state (higher RH lowered particle viscosity) and Fenton-type chemistry which resulted in the formation of reactive oxygen species, respectively. Such findings serve to emphasize the importance of ambient RH, the phase state of particle-bound organics in general, and the presence of coexisting metallic species for an accurate description of the degradation kinetics and aging of particulate OPFRs in models used to evaluate their atmospheric persistence.