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Zádor, Judit

Publications and source records attributed to Zádor, Judit.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Analytical ab initio hessian from a deep learning potential for transition state optimization

Identifying transition states—saddle points on the potential energy surface connecting reactant and product minima—is central to predicting kinetic barriers and understanding chemical reaction mechanisms. In this work, we train a fully differentiable equivariant neural network potential, NewtonNet, on thousands of organic reactions and derive the analytical Hessians. By reducing the computational cost by several orders of magnitude relative to the density functional theory (DFT) ab initio source, we can afford to use the learned Hessians at every step for the saddle point optimizations. We show that the full machine learned (ML) Hessian robustly finds the transition states of 240 unseen organic reactions, even when the quality of the initial guess structures are degraded, while reducing the number of optimization steps to convergence by 2–3× compared to the quasi-Newton DFT and ML methods. All data generation, NewtonNet model, and ML transition state finding methods are available in an automated workflow.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Gas-Phase Oxidation Mechanisms of Nitrogen-Containing Organic Compounds

Nitrogen-containing organic molecules play essential roles in nearly every aspect of chemistry. The importance of these species within gas-phase chemistry has increased in recent years, due to their emissions from wildfires, crude biofuels, ammonia combustion, and CO 2 capture facilities. However, there is a lack of detailed relevant mechanistic and kinetic studies of N-compounds, resulting in poor representation of these pathways within chemical models. In this report, we detail our exploration of the gas-phase oxidation mechanisms of pyrrole, imidazole, pyrrolidine, methylamine, and dimethylamine, done by employing multiplexed VUV photoionization mass spectrometry coupled with KinBot, a computational tool that automatically explores multi-well potential energy surfaces. Overall, we vastly expanded the known gas-phase oxidation mechanisms and chemical kinetics of these species. This work will improve the accuracy and completeness of atmospheric and combustion chemistry models, ultimately leading to better-informed decision-makers in the energy and environmental sectors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Density functional theory (DFT) study of UF 6 hydrolysis: reaction pathways, spectroscopy, and chemical kinetics

Depleted uranium hexafluoride (UF 6 ), a stockpiled byproduct of the nuclear fuel cycle, reacts readily with atmospheric humidity, but the gas-phase reaction mechanism and associated chemical kinetics are poorly understood. During the performance period we undertook development of a state-of-the-art ab initio gas-phase chemical kinetics simulation workflow to model the hydrolysis of uranium hexafluroride (UF 6 ). In doing so, we addressed several outstanding issues in the theoretical treatment of uranium-containing systems. At the outset it was unclear how to generate accurate estimates of kinetic and thermodynamic data for U-containing chemical reactions. Generation of such data has been made routine. Prior to our work, the literature associated with UF 6 hydrolysis were disparate and inaccurate. This body of work provides a modern and comprehensive theoretical assessment of the reaction mechanism, molecular clustering towards deposition, and chemical kinetics. New methodological implementations and software integrations resulting from this work are also highlighted. As much as possible, our predictions were validated against experimental data including particle morphologies, vibrational spectroscopy, atomization enthalpies, and kinetic rate constants. Nevertheless, we were unable to reconcile kinetic measurements with high-accuracy simulations.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2024

Theoretical analysis of the OH-initiated atmospheric oxidation reactions of imidazole

Imidazoles are present in Earth's atmosphere in both the gas-phase and in aerosol particles, and have been implicated in the formation of brown carbon aerosols. The gas-phase oxidation of imidazole (C 3 N 2 H 4 ) by hydroxyl radicals has been shown to be preferentially initiated via OH-addition to position C5, producing the 5-hydroxyimidazolyl radical adduct. However, the fate of this adduct upon reaction with O 2 in the atmospheric gas-phase is currently unknown. We employed an automated approach to investigate the reaction mechanism and kinetics of imidazole's OH-initiated gas-phase oxidation, in the presence of O 2 and NO x . The explored mechanism included reactions available to first-generation RO 2 radicals, as well as alkoxyl radicals produced from RO 2 + NO reactions. Product distributions were obtained by assembling and solving a master equation, under conditions relevant to the Earth's atmosphere. Our calculations show a complex, branched reaction mechanism, which nevertheless converges to yield two major closed-shell products: 4H-imidazol-4-ol (4H-4ol) and N,N′-diformylformamidine (FMF). At 298 K and 1 atm, we estimate the yields of 4H-4ol and FMF from imidazole oxidation initiated via OH-addition to position C5 to be 34 : 66, 12 : 85 and 2 : 95 under 10 ppt, 100 ppt and 1 ppb of NO respectively. This work also revealed O 2 -migration pathways between the α-N-imino peroxyl radical isomers. This reaction channel is fast for the first-generation RO 2 radicals, and may be important during the atmospheric oxidation of other unsaturated organic nitrogen compounds as well.

Almeida, Thomas Golin↗
DOE OSTI2024

Diffusion-Limited Kinetics in Reactive Systems

A proper representation of chemical kinetics is vital to understanding, modeling, and optimizing many important chemical processes. In liquid and surface phases, where diffusion is slow, the rate at which the reactants diffuse together limits the overall rate of many elementary reactions. Commonly, the textbook Smoluchowski theory is utilized to estimate effective rate coefficients in the liquid phase. On surfaces, modelers commonly resort to much more complex and expensive Kinetic Monte Carlo (KMC) simulations. Here, in this study, we extend the Smoluchowski model to allow the diffusing species to undergo chemical reactions and derive analytical formulas for the diffusion-limited rate coefficients for 3D, 2D, and 2D/3D interface cases. With these equations, we are able to demonstrate that when species react faster than they diffuse they can react orders of magnitude faster than predicted by Smoluchowski theory, through what we term “the reactive transport effect”. We validate the derived steady-state equations against particle Monte Carlo (PMC) simulations, KMC simulations, and non-steady-state solutions. Furthermore, using PMC and KMC simulations, we propose corrections that agree with all limits and the computed data for the 2D and 2D/3D interface steady-state equations, accounting for unique limitations in the associated derived equations. Additionally, we derive equations to handle couplings between diffusion-limited rate coefficients in reaction networks. We believe these equations should make it possible to run much more accurate mean-field simulations of liquids, surfaces, and liquid–surface interfaces accounting for diffusion limitations and the reactive transport effect.

Johnson, Matthew Sean↗
DOE OSTI2024

The photoionization of methoxymethanol: Fingerprinting a reactive C 2 oxygenate in a complex reactive mixture

Methoxymethanol (CH 3 OCH 2 OH) is a reactive C 2 ether-alcohol that is formed by coupling events in both heterogeneous and homogeneous systems. It is found in complex reactive environments—for example those associated with catalytic reactors, combustion systems, and liquid-phase mixtures of oxygenates. Using tunable synchrotron-generated vacuum-ultraviolet photons between 10.0 and 11.5 eV, we report on the photoionization spectroscopy of methoxymethanol. We determine that the lowest-energy photoionization process is the dissociative ionization of methoxymethanol via H-atom loss to produce [C 2 H 5 O 2 ] + , a fragment cation with a mass-to-charge ratio (m/z) = 61.029. Here, we measure the appearance energy of this fragment ion to be 10.24 ± 0.05 eV. The parent cation is not detected in the energy range examined. To elucidate the origin of the m/z = 61.029 (C 2 H 5 O 2 ) fragment, we used automated electronic structure calculations to identify key stationary points on the cation potential energy surface and compute conformer-specific microcanonical rate coefficients for the important unimolecular processes. The calculated H-atom dissociation pathway results in a [C 2 H 5 O 2 ] + fragment appearance at 10.21 eV, in excellent agreement with experimental results.

Hansen, Niko A.↗
DOE OSTI2024

Reaction dynamics of S( 3 P) with 1,3-butadiene and isoprene: crossed-beam scattering, low-temperature flow experiments, and high-level electronic structure calculations

Sulfur atoms serve as key players in diverse chemical processes, from astrochemistry at very low temperature to combustion at high temperature. Building upon our prior findings, showing cyclization to thiophenes following the reaction of ground-state sulfur atoms with dienes, we here extend this investigation to include many additional reaction products, guided by detailed theoretical predictions. The outcomes highlight the complex formation of products during intersystem crossing (ISC) to the singlet surfaces. Here, we employed crossed-beam velocity map imaging and high-level ab initio methods to explore the reaction of S( 3 P) with 1,3-butadiene and isoprene under single-collision conditions and in low-temperature flows. For the butadiene reaction, our experimental results show the formation of thiophene via H 2 loss, a 2H-thiophenyl radical through H loss, and thioketene through ethene loss at a slightly higher collision energy compared to previous observations. Complementary Chirped-Pulse Fourier-Transform mmWave spectroscopy (CP-FTmmW) measurements in a uniform flow confirmed the formation of thioketene in the reaction at 20 K. For the isoprene reaction, we observed analogous products along with the 2H-thiophenyl radical arising from methyl loss and C 3 H 4 S (loss of ethene or H 2 + acetylene). CP-FTmmW detected the formation of thioformaldehyde via loss of 1,3-butadiene, again in the 20 K flow. Coupled-cluster calculations on the pathways found by the automated kinetic workflow code KinBot support these findings and indicate ISC to the singlet surface, leading to the generation of various long-lived intermediates, including 5-membered heterocycles.

Lang, Jinxin↗
DOE OSTI2023

Dedication to James A. Miller

This special memorial issue pays tribute to James (Jim) A. Miller, a giant of combustion science who died in 2021, with a celebration of his enormous influence on the field. We were touched by the responses we received after we sent out the invitations for it. Jim inspired several generations of scientists, who viewed him as a mentor, a father figure, and a friend. Together with Nils Hansen and Peter Glarborg, we have written a detailed account on his life and work. Furthermore, it appeared in this journal shortly after his death; and so here we focus on the scientific areas he had interest in and influence on, and how they relate to the 34 papers in this issue. The topics of these papers span a variety of Jim's interests including nitrogen chemistry, polycyclic aromatic hydrocarbon (PAH) chemistry, oxidation chemistry, energy transfer, prompt dissociations, and codes to facilitate combustion chemistry simulations.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2023

Sulfur ( 3 P) Reaction with Conjugated Dienes Gives Cyclization to Thiophenes under Single Collision Conditions

Here, we combine crossed-beam velocity map imaging with high-level ab initio/transition state theory modeling of the reaction of S( 3 P) with 1,3-butadiene and isoprene under single collision conditions. For the butadiene reaction, we detect both H and H 2 loss from the initial adduct, and from reaction with isoprene, we see both H loss and methyl loss. Theoretical calculations confirm these arise following intersystem crossing to the singlet surface forming long-lived intermediates. For the butadiene reaction, these lose H 2 to form thiophene as the dominant channel, H to form the detected 2H-thiophenyl radical, or ethene, giving thioketene. For isoprene, additional reaction products are suggested by theory, including the observed H and methyl loss radicals, but also methyl thiophene, thioformaldehyde, and thioketene. The results for S( 3 P) + 1,3-butadiene, showing direct cyclization to the aromatic product and yielding few bimolecular product channels, are in striking contrast to those for the analogous O( 3 P) reaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Pynta-An Automated Workflow for Calculation of Surface and Gas-Surface Kinetics

Many important industrial processes rely on heterogeneous catalytic systems. However, given all possible catalysts and conditions of interest, it is impractical to optimize most systems experimentally. Automatically generated microkinetic models can be used to efficiently consider many catalysts and conditions. However, these microkinetic models require accurate estimation of many thermochemical and kinetic parameters. Manually calculating these parameters is tedious and error prone, involving many interconnected computations. Here, we present Pynta, a workflow software for automating the calculation of surface and gas–surface reactions. Pynta takes the reactants, products, and atom maps for the reactions of interest, generates sets of initial guesses for all species and saddle points, runs all optimizations, frequency, and IRC calculations, and computes the associated thermochemistry and rate coefficients. It is able to consider all unique adsorption configurations for both adsorbates and saddle points, allowing it to handle high index surfaces and bidentate species. Pynta implements a new saddle point guess generation method called harmonically forced saddle point searching (HFSP). HFSP defines harmonic potentials based on the optimized adsorbate geometries and which bonds are breaking and forming that allow initial placements to be optimized using the GFN1-xTB semiempirical method to create reliable saddle point guesses. This method is reaction class agnostic and fast, allowing Pynta to consider all possible adsorbate site placements efficiently. We demonstrate Pynta on 11 diverse reactions involving monodenate, bidentate, and gas-phase species, many distinct reaction classes, and both a low and a high index facet of Cu. Our results suggest that it is very important to consider reactions between adsorbates adsorbed in all unique configurations for interadsorbate group transfers and reactions on high index surfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Multifidelity Neural Network Formulations for Prediction of Reactive Molecular Potential Energy Surfaces

Here, this paper focuses on the development of multifidelity modeling approaches using neural network surrogates, where training data arising from multiple model forms and resolutions are integrated to predict high-fidelity response quantities of interest at lower cost. We focus on the context of quantum chemistry and the integration of information from multiple levels of theory. Important foundations include the use of symmetry function-based atomic energy vector constructions as feature vectors for representing structures across families of molecules and single-fidelity neural network training capabilities that learn the relationships needed to map feature vectors to potential energy predictions. These foundations are embedded within several multifidelity topologies that decompose the high-fidelity mapping into model-based components, including sequential formulations that admit a general nonlinear mapping across fidelities and discrepancy-based formulations that presume an additive decomposition. Methodologies are first explored and demonstrated on a pair of simple analytical test problems and then deployed for potential energy prediction for C 5 H 5 using B2PLYP-D3/6-311++G(d,p) for high-fidelity simulation data and Hartree–Fock 6-31G for low-fidelity data. For the common case of limited access to high-fidelity data, our computational results demonstrate that multifidelity neural network potential energy surface constructions achieve roughly an order of magnitude improvement, either in terms of test error reduction for equivalent total simulation cost or reduction in total cost for equivalent error.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Comprehensive Kinetics on the C 7 H 7 Potential Energy Surface under Combustion Conditions

The automated kinetics workflow code, KinBot, was used to explore and characterize the regions of the C 7 H 7 potential energy surface that are relevant to combustion environments and especially soot inception. We first explored the lowest-energy region, which includes the benzyl, fulvenallene + H, and cyclopentadienyl + acetylene entry points. We then expanded the model to include two higher-energy entry points, vinylpropargyl + acetylene and vinylacetylene + propargyl. The automated search was able to uncover the pathways from the literature. In addition, three important new routes were discovered: a lower-energy pathway connecting benzyl with vinylcyclopentadienyl, a decomposition mechanism from benzyl that results in side-chain hydrogen atom loss to produce fulvenallene + H, and shorter and lower energy routes to the dimethylene-cyclopentenyl intermediates. We systematically reduced the extended model to a chemically relevant domain composed of 63 wells, 10 bimolecular products, 87 barriers, and 1 barrierless channel and constructed a master equation using the CCSD(T)-F12a/cc-pVTZ//ωB97X-D/6-311++G(d,p) level of theory to provide rate coefficients for chemical modeling. Our calculated rate coefficients show excellent agreement with measured ones. We also simulated concentration profiles and calculated branching fractions from the important entry points to provide an interpretation of this important chemical landscape.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Automated Reaction Kinetics of Gas-Phase Organic Species over Multiwell Potential Energy Surfaces

Automation of rate-coefficient calculations for gas-phase organic species became possible in recent years and has transformed how we explore these complicated systems computationally. Kinetics workflow tools bring rigor and speed and eliminate a large fraction of manual labor and related error sources. In this paper we give an overview of this quickly evolving field and illustrate, through five detailed examples, the capabilities of our own automated tool, KinBot. Here we bring examples from combustion and atmospheric chemistry of C-, H-, O-, and N-atom-containing species that are relevant to molecular weight growth and autoxidation processes. The examples shed light on the capabilities of automation and also highlight particular challenges associated with the various chemical systems that need to be addressed in future work.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Formation of Organic Acids and Carbonyl Compounds in n ‐Butane Oxidation via γ‐Ketohydroperoxide Decomposition

Abstract A crucial chain‐branching step in autoignition is the decomposition of ketohydroperoxides (KHP) to form an oxy radical and OH. Other pathways compete with chain‐branching, such as “Korcek” dissociation of γ‐KHP to a carbonyl and an acid. Here we characterize the formation of a γ‐KHP and its decomposition to formic acid+acetone products from observations of n ‐butane oxidation in two complementary experiments. In jet‐stirred reactor measurements, KHP is observed above 590 K. The KHP concentration decreases with increasing temperature, whereas formic acid and acetone products increase. Observation of characteristic isotopologs acetone‐ d 3 and formic acid‐ d 0 in the oxidation of CH 3 CD 2 CD 2 CH 3 is consistent with a Korcek mechanism. In laser‐initiated oxidation experiments of n ‐butane, formic acid and acetone are produced on the timescale of KHP removal. Modelling the time‐resolved production of formic acid provides an estimated upper limit of 2 s −1 for the rate coefficient of KHP decomposition to formic acid+acetone.

Popolan‐Vaida, Denisia M.↗
DOE OSTI2022

Formation of Organic Acids and Carbonyl Compounds in $\textit{n}$-Butane Oxidation via γ-Ketohydroperoxide Decomposition

A crucial chain-branching step in autoignition is the decomposition of ketohydroperoxides (KHP) to form an oxy radical and OH. Other pathways compete with chain-branching, such as “Korcek” dissociation of γ-KHP to a carbonyl and an acid. Here we characterize the formation of a γ-KHP and its decomposition to formic acid+acetone products from observations of $\textit{n}$-butane oxidation in two complementary experiments. In jet-stirred reactor measurements, KHP is observed above 590 K. The KHP concentration decreases with increasing temperature, whereas formic acid and acetone products increase. Observation of characteristic isotopologs acetone-$d_3$ and formic acid-$d_0$ in the oxidation of CH 3 CD 2 CD 2 CH 3 is consistent with a Korcek mechanism. In laser-initiated oxidation experiments of $\textit{n}$-butane, formic acid and acetone are produced on the timescale of KHP removal. Further, modelling the time-resolved production of formic acid provides an estimated upper limit of 2 s –1 for the rate coefficient of KHP decomposition to formic acid+acetone.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗