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Explaining persistent incomplete mixing in multicomponent reactive transport with Eulerian stochastic model

We present an Eulerian stochastic advection–diffusion–reaction (SADR) model and use it to explain incomplete mixing typically observed in transport experiments with bimolecular reactions. Unlike traditional advection– dispersion–reaction (ADR) models, the SADR model describes mechanical and diffusive mixing as two separate processes. In the SADR model, mechanical mixing is driven by random advective velocity whose variance is given by the coefficient of mechanical dispersion. The diffusive mixing is modeled as a Fickian diffusion process with the effective diffusion coefficient. We demonstrate that the sum of the two coefficients is equal to the dispersion coefficient, but only the effective diffusion coefficient contributes to the mixing-controlled reactions. We use experimental results of Gramling et al. * * to show that for transport and bimolecular reactions in porous media, the SADR model is significantly more accurate than the ADR model, which overestimates the concentration of the reaction product by as much as 60%. We also show that the SADR model predicts an experimentally observed bell- shaped spatial distribution of the reactive product concentration, while the ADR model results in a concentration distribution with an unphysical kink.

Bimolecular reactions, incomplete mixing, Stochast↗

Photoinitiated Reactions of Molecules and Radicals in Molecular Beams

The UV photochemistry of organic molecules is a fundamental process that governs reactions in the atmosphere, synthetic chemistry, processing of organic aerosols, and biological damage in living tissues. In many organic molecules, the ensuing evolution involves pathways that are in competition, giving rise to different products, isomerization, coupling to other electronic states, and secondary reactive collisions. Because photodissociation is usually fast (picoseconds to microseconds), these processes are far from equilibrium and are controlled by kinetic competition and dynamical forces. The work accomplished was focused primarily on the photochemistry of alpha-keto carboxylic acids, a group of acids produced from natural sources, which are implicated in aerosol formation and biological processes. In the atmosphere, they are destroyed mainly by solar radiation. Studying their photochemistry has been surprisingly difficult because of the complexity of their excited electronic states, and the effect of collisions and secondary reactions. The second project investigated the lifetime of excited electronic states of pyrazine and picoline and had both experimental and theoretical aspects. The work focused on a model molecule, pyruvic acid (PA), because it was hypothesized that it should be a good source of the unstable carbene, methylhydroxycarbene (MHC). PA has an internal hydrogen bond that controls the evolution of its decomposition. The decomposition was studied following excitation to two of its lowest excited states reached by laser irradiation at 351 and 193 nm. The photodissociation dynamics in the absence and presence of collisions was monitored and compared. Understanding the UV photochemistry requires the use of complementary experimental approaches. Two methods were enlisted, which together generated a comprehensive and detailed set of results: (i) The time-sliced velocity map imaging (SVMI) instrument at USC was exploited to determine kinetic energy release of fragments, fast dissociation timescales, and internal state distributions of fragments for which Resonance Enhanced Multiphoton Ionization (REMPI) schemes exist; and (ii) The multiplexed photoionization mass spectrometer (MPIMS) setup developed at the Sandia Combustion Research Facility was used for product discovery, achieved by exploiting tunable narrowband VUV radiation at the Advanced Light Source (ALS), and to follow in real time their subsequent unimolecular and bimolecular reactions. The experimental conditions ranged from collisionless molecular beams to study nascent products to flow reactors of variable pressures to study subsequent bimolecular reactions of the products. The goals stated above were successfully accomplished. By exciting PA to its lowest excited state, MHC was identified as the only primary product and its isomerization to vinylalcohol and acetaldehyde was directly observed in real time. Moreover, we reported the first bimolecular reaction of MHC, which was with acetaldehyde, and identified its reaction product. This paves the way for the study of other reactions of this important carbene intermediate. When excitation was carried out at 193 nm, which imparted much higher energy to PA, many more products were directly observed in real time, some deriving from three-body dissociation. Quantitative branching ratios and secondary reactions of radical products were also determined and analyzed. The studies of pyrazine and picoline focused on the second excited state of these molecules and showed (via ionization studies) that their excited states were very short lived (<100 fs) because of efficient couplings to lower electronic states via vibronic coupling. Theoretical work on modeling the absorption spectrum and decay mechanisms of the excited states are in progress in collaboration with theoreticians.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Criegee Intermediates Compete Well with OH as a Cleaning Agent for Atmospheric Amides

Elucidating the chemical kinetics of stabilized Criegee intermediates (sCIs) in the atmosphere is critically important for climate modeling. Here, we report a class of very rapid bimolecular reactions of two sCIs, namely, CH 2 OO and syn-CH 3 CHOO, with amides. We used electronic structure calculations and kinetics calculations to elucidate a universal mechanism by which the oxygen atom of the carbonyl group in an amide is added to the carbon atom of the COO group in the sCI with simultaneous transfer of the amide hydrogen to the terminal oxygen atom of the carbonyl oxide of the sCI. The barriers for the mechanism are submerged below reactants by ∼9 kcal/mol, which means that the tight transition state is not the rate-determining step, and the rate constants are determined by loose free energy bottlenecks between the reactants and the precursor complexes. We calculate the rate constants due to these loose and barrierless transition states by variable-reaction-coordinate variational transition-state theory. We find that bimolecular reactions of sCIs with amides are very rapid, with rate constants 1 to 5 × 10 –10 cm 3 molecule –1 s –1 , which is a factor of 2 faster than the rate constants of carboxylic acids with sCIs and 10 2 faster than the rate constants of OH reactions with amides. This has the consequence that, under a wide range of conditions, sCIs are the major sink for atmospheric amides, in contrast to the usual assumption that OH radicals are the dominant sinks.

Amides↗

Directed gas phase preparation of ethynylallene (H 2 CCCHCCH; X 1 A') via the crossed molecular beam reaction of the methylidyne radical (CH; X 2 Π) with vinylacetylene (H 2 CCHCCH; X 1 A')

The gas-phase bimolecular reaction of the methylidyne (CH; X 2 Π) radical with vinylacetylene (H 2 CCHCCH; X 1 A') was conducted at a collision energy of 20.3 kJ mol –1 under single collision conditions exploiting the crossed molecular beam experimental results merged with ab initio electronic structure calculations and ab initio molecular dynamics (AIMD) simulations. The laboratory data reveal that the bimolecular reaction proceeds barrierlessly via indirect scattering dynamics through long-lived C 5 H 5 reaction intermediate(s) ultimately dissociating to C 5 H 4 isomers along with atomic hydrogen with the latter predominantly originating from the vinylacetylene reactant as confirmed by the isotopic substitution experiments in the D1-methylidyne–vinylacetylene reaction. Combined with ab initio calculations of the potential energy surface (PES) and statistical Rice–Ramsperger–Kassel–Marcus (RRKM) calculations, the experimental determined reaction energy of –146 ± 26 kJ mol –1 along with the distribution minimum of T(θ) at 90° and isotopic substitution experiments suggest ethynylallene (p1; ΔrG = –230 ± 4 kJ mol –1 ) as the dominant product. The ethynylallene (p1) may be formed with extensive rovibrational excitation, which would result in a lower maximum translational energy. Further, AIMD simulations reveal that the reaction dynamics leads to p1 (ethynylallene, 75%) plus atomic hydrogen with the dominant initial complex being i1 formed by methylidyne radical addition to the double C[double bond, length as m-dash]C bond in vinylacetylene. Altogether, combining the crossed molecular beam experimental results with ab initio electronic structure calculations and ab initio molecular dynamics (AIMD) simulations, ethynylallene (p1) is expected to represent the dominant product in the reaction of the methylidyne (CH; X 2 Π) radical with vinylacetylene (H 2 CCHCCH; X 1 A').

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Oxidation and pyrolysis of methyl propyl ether

The ignition, oxidation, and pyrolysis chemistry of methyl propyl ether (MPE) was probed experimentally at several different conditions, and a comprehensive chemical kinetic model was constructed to help understand the observations, with many of the key parameters computed using quantum chemistry and transition state theory. Experiments were carried out in a shock tube measuring time variation of CO concentrations, in a flow tube measuring product concentrations, and in a rapid compression machine (RCM) measuring ignition delay times. The detailed reaction mechanism was constructed using the Reaction Mechanism Generator software. Sensitivity and flux analyses were used to identify key rate and thermochemical parameters, which were then computed using quantum chemistry to improve the mechanism. Validation of the final model against the 1-20 bar 600-1500 K experimental data is presented with a discussion of the kinetics. The model is in excellent agreement with most of the shock tube and RCM data. Strong non-monotonic variation in conversion and product distribution is observed in the flow-tube experiments as the temperature is increased, and unusually strong pressure dependence and significant heat release during the compression stroke is observed in the RCM experiments. These observations are largely explained by a close competition between radical decomposition and addition to O2 at different sites in MPE; this causes small shifts in conditions to lead to big shifts in the dominant reaction pathways. The validated mechanism was used to study the chemistry occurring during ignition in a diesel engine, simulated using Ignition Quality Test (IQT) conditions. At the IQT conditions, where the MPE concentration is higher, bimolecular reactions of peroxy radicals are much more important than in the RCM.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Graph characterization of higher-order structure in atmospheric chemical reaction mechanisms

Atmospheric chemical reactions play an important role in air quality and climate change. While the structure and dynamics of individual chemical reactions are fairly well understood, the emergent properties of the entire atmospheric chemical system, which can involve many different species that participate in many different reactions, are not well described. In this work, we leverage graph-theoretic techniques to characterize patterns of interaction (“motifs”) in three different representations of gas-phase atmospheric chemistry, termed “chemical mechanisms.” These widely used mechanisms, the master chemical mechanism, the GEOS-Chem mechanism, and the Super-Fast mechanism, vary dramatically in scale and application, but they all generally aim to simulate the abundance and variability of chemical species in the atmosphere. This motif analysis quantifies the fundamental patterns of interaction within the mechanisms, which are directly related to their construction. For example, the gas-phase chemistry in the very small Super-Fast mechanism is entirely composed of bimolecular reactions, and its motif distribution matches that of an individual bimolecular reaction well. The larger and more complex mechanisms show emergent motif distributions that differ strongly from any specific reaction type, consistent with their complexity. The proposed motif analysis demonstrates that while these mechanisms all have a similar design goal, their higher-order structure of interactions differs strongly and thus provides a novel set of tools for exploring differences across chemical mechanisms.

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An extended methodology for automated calculations of non-Boltzmann kinetic sequences: H + C 2 H 2 + X and combustion impact

It is generally assumed in phenomenological kinetic models that bimolecular reactions only occur between species whose rovibrational energy follows a Boltzmann (thermal) distribution. That is, any complexes initially formed in non-Boltzmann distributions are assumed to be thermalized by energy-transferring collisions prior to bimolecular reactions. Given the high mole fractions of reactive species, X, in combustion environments, reactive collisions of the complexes with X often occur on the same timescale as energy-transferring collisions – yielding sequences proceeding through non-Boltzmann intermediates across multiple potential energy surfaces. Recent studies have shown that such non-Boltzmann kinetic sequences can have substantial impact on the global reactivity in combustion systems. Simulations of these non-Boltzmann reaction sequences, which can be described in phenomenological kinetic models via chemically termolecular reactions, require that rovibrational excitation from one potential energy surface be carried over to the next. Here this paper presents an extended theoretical and computational methodology that couples multiple master equations and derives rate constants for phenomenological reactions describing the conversion of thermal reactants to thermal products for use in phenomenological kinetic schemes. The methodology is then implemented using in-house scripts for non-Boltzmann sequences involving C2H$^*_3$ + X (with X = O 2 , H, and OH) where C 2 H$^*_3$ is formed via H + C 2 H 2 association – which were identified as having strong potential for influencing combustion predictions in a recent study. The results reveal that non-Boltzmann reaction sequences for X = O 2 (the primary focus of this paper) significantly alters the total conversion rate from H + C 2 H 2 to products and product branching fractions from those of thermal sequential pathways. Furthermore, the present results demonstrate that non-Boltzmann reaction sequences have significant impact – as high as an order of magnitude – on predicted ignition delay times. Similarly, they yield significantly different dependence of ignition delay times with temperature and O 2 mole fraction – yielding signatures that are likely observable experimentally.

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From the laboratory to space: unveiling isomeric diversity of C 5 H 2 in the reaction of tricarbon (C 3 , X 1 Σ g + ) with the vinyl radical (C 2 H 3 , X 2 A′)

By connecting laboratory dynamics with cosmic observables, this work highlights the critical role of reactions between highly reactive species in shaping the molecular inventory of the interstellar medium and opens new windows into the spectroscopically elusive corners of astrochemical complexity. The gas phase formation of distinct C 5 H 2 isomers is explored through the bimolecular reaction of tricarbon (C 3 , X 1 Σ + g ) with the vinyl radical (C 2 H 3 , X 2 A′) at a collision energy of 44 ± 1 kJ mol −1 employing the crossed molecular beam technique augmented by electronic structure and Rice–Ramsperger–Kassel–Marcus (RRKM) calculations. This barrierless and exoergic reaction follows indirect dynamics and is initiated by the addition of tricarbon to the radical center of the vinyl radical forming a Cs symmetric doublet collisional complex (CCCCHCH 2 ). Subsequent low-barrier isomerization steps culminate in the resonantly stabilized 2,4-pentadiynyl-1 radical (CHCCCCH 2 ), which decomposes via atomic hydrogen loss. Statistical calculations identify linear, triplet pentadiynylidene (p2, X 3 Σ − g ) as the dominant product, while singlet carbenes ethynylcyclopropenylidene (p1, X 1 A′), pentatetraenylidene (p3, X 1 A 1 ), and ethynylpropadienylidene (p4, X 1 A′) are formed with lower branching ratios. The least stable isomer, 2-cyclopropen-1-ylidenethenylidene (‘eiffelene’; p5, X 1 A 1 ), remains thermodynamically feasible, but exhibits negligible branching ratios. Two isomers detected in TMC-1 to date (p1 and p3) possess significant dipole moments making them amenable to radio telescopic observations, whereas linear pentadiynylidene (p2; D ∞h ) is only traceable via infrared spectroscopy or through its cyanopentadiynylidene derivative (HCCCCCCN). This study highlights the isomer diversity accessed in the low temperature hydrocarbon chemistry of barrierless and exoergic bimolecular reactions involving two unstable, reactants in cold molecular clouds.

Medvedkov, Iakov A. [University of Hawai'i at Mano↗

Formic acid catalyzed isomerization and adduct formation of an isoprene-derived Criegee intermediate: experiment and theory

Isoprene is the most abundant non-methane hydrocarbon emitted into the Earth's atmosphere. Ozonolysis is an important atmospheric sink for isoprene, which generates reactive carbonyl oxide species (R 1 R 2 C[double bond, length as m-dash]O + O – ) known as Criegee intermediates. This study focuses on characterizing the catalyzed isomerization and adduct formation pathways for the reaction between formic acid and methyl vinyl ketone oxide (MVK-oxide), a four-carbon unsaturated Criegee intermediate generated from isoprene ozonolysis. syn-MVK-oxide undergoes intramolecular 1,4 H-atom transfer to form a substituted vinyl hydroperoxide intermediate, 2-hydroperoxybuta-1,3-diene (HPBD), which subsequently decomposes to hydroxyl and vinoxylic radical products. In this paper, we report direct observation of HPBD generated by formic acid catalyzed isomerization of MVK-oxide under thermal conditions (298 K, 10 torr) using multiplexed photoionization mass spectrometry. The acid catalyzed isomerization of MVK-oxide proceeds by a double hydrogen-bonded interaction followed by a concerted H-atom transfer via submerged barriers to produce HPBD and regenerate formic acid. The analogous isomerization pathway catalyzed with deuterated formic acid (D2-formic acid) enables migration of a D atom to yield partially deuterated HPBD (DPBD), which is identified by its distinct mass (m/z 87) and photoionization threshold. In addition, bimolecular reaction of MVK-oxide with D 2 -formic acid forms a functionalized hydroperoxide adduct, which is the dominant product channel, and is compared to a previous bimolecular reaction study with normal formic acid. Complementary high-level theoretical calculations are performed to further investigate the reaction pathways and kinetics.

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Reactive Transport Modeling with Physics-Informed Machine Learning for Critical Minerals Applications

This study presents a physics-informed neural network (PINN) framework for reactive transport modeling for simulating fast bimolecular reactions in porous media. Accurate characterization of cAhemical interactions and product formation in surface and subsurface environments is essential for advancing critical mineral extraction and related geoscience applications. The proposed methodology sequentially addresses the flow and diffusion–reaction subproblems. The flow field is computed using a mixed formulation, while the diffusion–reaction system is modeled via two uncoupled tensorial diffusion equations reformulated in terms of chemical invariants. PINNs are employed to solve the governing equations, enabling data-efficient, mesh-free prediction of chemical concentration fields. The framework is validated through a series of benchmark problems involving flow in heterogeneous porous media. Initial verification is conducted using patch tests for the flow field, followed by validation of the transport problem with emphasis on preserving non-negativity of concentrations. The complete fast bimolecular reaction scenario is then solved, yielding spatial distributions of reactants and product species. Results demonstrate that the PINNs-based approach effectively captures sharp, mixing-limited reaction fronts and dispersive mixing behavior, offering reliable predictions of reactive plume evolution. These capabilities are crucial for evaluating long-term subsurface behavior in applications such as fluid storage, energy extraction, and efficient extraction of critical minerals.

42 ENGINEERING↗

Ultrafast dynamics of CN radical reactions with chloroform solvent under vibrational strong coupling

Polariton chemistry may provide a new means to control molecular reactivity, permitting remote, reversible modification of reaction energetics, kinetics, and product yields. A considerable body of experimental and theoretical work has already demonstrated that strong coupling between a molecular vibrational mode and the confined electromagnetic field of an optical cavity can alter chemical reactivity without external illumination. However, the mechanisms underlying cavity-altered chemistry remain unclear in large part because the experimental systems examined previously are too complex for detailed analysis of their reaction dynamics. Here, we experimentally investigate photolysis-induced reactions of cyanide radicals with strongly-coupled chloroform (CHCl 3 ) solvent molecules and examine the intracavity rates of photofragment recombination, solvent complexation, and hydrogen abstraction. Here we use a microfluidic optical cavity fitted with dichroic mirrors to facilitate vibrational strong coupling (VSC) of the C–H stretching mode of CHCl 3 while simultaneously permitting optical access at visible wavelengths. Ultrafast transient absorption experiments performed with cavities tuned on- and off-resonance reveal that VSC of the CHCl 3 C–H stretching transition does not significantly modify any measured rate constants, including those associated with the hydrogen abstraction reaction. This work represents, to the best of our knowledge, the first experimental study of an elementary bimolecular reaction under VSC. We discuss how the conspicuous absence of cavity-altered effects in this system may provide insights into the mechanisms of modified ground state reactivity under VSC and help bridge the divide between experimental results and theoretical predictions in vibrational polariton chemistry.

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Probing the dynamics and bottleneck of the key atmospheric SO 2 oxidation reaction by the hydroxyl radical

SO 2 (Sulfur dioxide) is the major precursor to the production of sulfuric acid (H 2 SO 4 ), contributing to acid rain and atmospheric aerosols. Sulfuric acid formed from SO 2 generates light-reflecting sulfate aerosol particles in the atmosphere. This property has prompted recent geoengineering proposals to inject sulfuric acid or its precursors into the Earth’s atmosphere to increase the planetary albedo to counteract global warming. SO 2 oxidation in the atmosphere by the hydroxyl radical HO to form HOSO 2 is a key rate-limiting step in the mechanism for forming acid rain. However, the dynamics of the HO + SO 2 → HOSO 2 reaction and its slow rate in the atmosphere are poorly understood to date. Herein, we use photoelectron spectroscopy of cryogenically cooled HOSO 2 – anion to access the neutral HOSO 2 radical near the transition state of the HO + SO 2 reaction. Spectroscopic and dynamic calculations are conducted on the first ab initio-based full-dimensional potential energy surface to interpret the photoelectron spectra of HOSO 2 – and to probe the dynamics of the HO + SO 2 reaction. In addition to the finding of a unique pre-reaction complex (HO⋯SO 2 ) directly connected to the transition state, dynamic calculations reveal that the accessible phase space for the HO + SO 2 → HOSO 2 reaction is extremely narrow, forming a key reaction bottleneck and slowing the reaction rate in the atmosphere, despite the low reaction barrier. This study underlines the importance of understanding the full multidimensional potential energy surface to elucidate the dynamics of complex bimolecular reactions involving polyatomic reactants.

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Stochastic self-tuning hybrid algorithm for reaction-diffusion systems

Many biochemical phenomena involve reactants with vastly different concentrations, some of which are amenable to continuum-level descriptions, while the others are not. We present a hybrid self-tuning algorithm to model such systems. The method combines microscopic (Brownian) dynamics for diffusion with mesoscopic (Gillespie-type) methods for reactions and remains efficient in a wide range of regimes and scenarios with large variations of concentrations. Furthermore, its accuracy, robustness, and versatility are balanced by redefining propensities and optimizing the mesh size and time step. We use a bimolecular reaction to demonstrate the potential of our method in a broad spectrum of scenarios: from almost completely reaction-dominated systems to cases where reactions rarely occur or take place very slowly. The simulation results show that the number of particles present in the system does not degrade the performance of our method. This makes it an accurate and computationally efficient tool to model complex multireaction systems.

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Pulsed laser photolysis study of the reaction between O(3P) and HO2

It is pointed out that bimolecular reactions involving two free radicals are of great interest because both reactants have unpaired electrons and hence could interact at distances longer than those typical of radical-molecule encounters. A method based on laser photolysis is being developed to produce selectively free radicals in the homogeneous gas phase. This is to be done in such a way as to isolate the reaction of interest and subsequently follow the course of the reaction using spectroscopic techniques. The present investigation is concerned with a study in which the rate coefficient for the reaction of O(3P) with HO2, has been measured at N2 pressures ranging from 10 to 500 torr, taking into account the reaction O(3P)+HO2 yields OH-O2. In the described study, O(3P) and HO2 were produced by cophotolysis of O3 and H2O2 in N2 at 248.5 nm using a KrF excimer laser.

Ravishankara, A. R.↗

Cool flame chemistry of diesel surrogate compounds: n -Decane, 2-methylnonane, 2,7-dimethyloctane, and n -butylcyclohexane

Elucidating the formation of combustion intermediates is crucial to validate reaction pathways, develop reaction mechanisms and examine kinetic modeling predictions. While high-temperature pyrolysis and oxidation intermediates of alkanes have been thoroughly studied, comprehensive analysis of cool flame intermediates from alkane autoxidation is lacking and challenging due to the complexity of intermediate species produced. Here, jet-stirred reactor autoxidation of four C 10 alkanes: n -decane, 2-methylnonane, 2,7-dimethyloctane, and n -butylcyclohexane, as model compounds of diesel fuel, was investigated from 500 to 630 K using synchrotron vacuum ultraviolet photoionization molecular beam mass spectrometry (SVUV-PIMS). Around 100 intermediates were detected for each fuel. The classes of molecular structures present during the autoxidation of the representative paraffinic functional groups in transport fuels, i.e., n -alkanes, branched alkanes, and cycloalkanes were established and were found to be similar from the oxidation of various alkanes. A theoretical approach was applied to estimate the photoionization cross sections of the intermediates with the same carbon skeleton as the reactants, e.g., alkene, alkenyl keto, cyclic ether, dione, keto-hydroperoxide, diketo-hydroperoxide, and keto-dihydroperoxide. These species are indicators of the first, second, and third O 2 addition reactions for the four C 10 hydrocarbons, as well as bimolecular reactions involving keto-hydroperoxides. Chemical kinetic models for the oxidation of these four fuels were examined by comparison against mole fraction of the reactants and final products obtained in additional experiments using gas chromatography analysis, as well as the detailed species pool and mole fractions of aforementioned seven types of intermediates measured by SVUV-PIMS. This works reveals that the models in the literature need to be improved, not only the prediction of the fuel reactivity and final products, but also the reaction network to predict the formation of many previous undetected intermediates.

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