Pynta─An Automated Workflow for Calculation of Surface and Gas–Surface Kinetics
This is our newest workflow code, this time we are interested in accelerating reaction discovery for heterogeneous catalysis. Pynta automates many of the usual, but tedious and error prone steps of this work. More crucially, it also features a new saddle point estimating algorithm, termed as harmonically forced saddle point (HFSP) search, which allows the fast generation of many site-specific saddle point guesses. There are filtered with a harmonic filter that aims to keep the lower energy ones only, to be submitted for a full DFT calculation.
Johnson, M. S., Gierada, M., Hermes, E. D., Bross, D. H., Sargsyan, K., Najm, H. N., Zádor, J.: Pynta - An automated workflow for calculation of surface and gas-surface kinetics. Journal of Chemical Information and Modeling, 2023. https://doi.org/10.1021/acs.jcim.3c00948
Sulfur (3P) Reaction with Conjugated Dienes Gives Cyclization to Thiophenes under Single Collision Conditions
In this collaboration with the group of Arthur Suits, we combined crossed-beam velocity map imaging with high-level ab initio/transition state theory modeling of the reaction of S(3P) with 1,3-butadiene and isoprene under single collision conditions. The most surprising outcome is the system's propensity to cyclize under these conditions, which is a process that is happening after intersystem crossing. The reaction showing direct cyclization to the aromatic product and yielding few bimolecular product channels, are in striking contrast to those for the analogous O(3P) reaction.
Comprehensive Kinetics on the C7H7 Potential Energy Surface under Combustion Conditions
The automated kinetics workflow code, KinBot, was used to explore and characterize the regions of the C7H7 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.
Martí, C., Michelsen, H. A., Najm, H. N., Zádor, J.: Comprehensive kinetics on the C7H7 potential energy surface under combustion conditions. Journal of Physical Chemistry A, 2023 127 1941–1959. https://doi.org/10.1021/acs.jpca.2c08035
Automated Reaction Kinetics of Gas-Phase Organic Species over Multiwell Potential Energy Surfaces
We are developing a complex workflow code, KinBot, to automate gas-phase chemical kinetics calculations. Our recent Feature Article in JPCA walks you through some examples to show its current capabilities. A more detailed, code-focused description is in the 2020 paper below.
Zádor, J., Martí, C., Van de Vijver, R., Johansen, S. L., Yang, Y., Michelsen, H. A., Najm, H. N., Automated reaction kinetics of gas-phase organic molecules. Journal of Physical Chemistry A Feature Article, 2023 127 565–588. https://doi.org/10.1021/acs.jpca.2c06558
Van de Vijver, R., Zádor, J.: KinBot: Automated stationary point search on potential energy surfaces. Computer Physics Communications, 2020 248 106947. https://doi.org/10.1016/j.cpc.2019.106947
Stereoisomer-dependent unimolecular kinetics
In collaboration with the group of Professor Brandon Rotavera (U Georgia) we used KinBot to explore the PESs and calculate rate coefficients for syn and anti stereoisomers of 2,4-dimethyloxetanyl peroxy radicals. We found that the stereochemistry of the alkyl substituents radicals significantly impacts the competition between conventional QOOH pathways and ring-opening reactions, and can completely restrict certain reaction pathways. On seven PESs we calculated more than 4,000 rate coefficients for any given temperature or pressure!
Doner, A. C., Zádor, J., Rotavera, B.: Stereoisomer-dependent unimolecular kinetics of 2,4-dimethyloxetane peroxy radicals. Faraday Discussions, 2022. https://doi.org/10.1039/D2FD00029F
unexpected product channels in the O(3P) + cyclopentene reaction
In collaboration with my experimental colleagues at Sandia, Drs. David L. Osborn and Krupa Ramasesha, we investigated the reaction of O(3P) with cyclopentene. We used the MPIMS machine and KinBot to unravel this complicated reaction that is happening over two PESs, the upper triplet and the lower singlet ones, by comparing experimental and calculated product yields. The quest for these types of reactions is often to understand which products are produced on which electronic surfaces. The generally held belief is that intersystem crossing is largely important around the initial triplet adduct, but here we found strong evidence for large intersystem crossing flux further away from it.
Ramasesha, K., Savee, J. D., Zádor, J., Osborn, D. L.: Multiplexed photoionization mass spectrometry studies of the O(3P) + cyclopentene reaction reveal unexpected product channels. Journal of Physical Chemistry A, 2021 125 9785-9801. https://doi.org/10.1021/acs.jpca.1c05817
Sella, an open-source automation-friendly molecular saddle point optimizer
We have implemented our highly efficient and flexible saddle point optimization algorithms in Sella, an open source software package. Sella has shown superior performance benchmarks, both for clusters of atoms and molecular systems. Sella is designed for use in automated frameworks, where robustness is key in addition to computational cost. Molecular structures are treated with a redundant internal coordinate system, which is automatically defined and includes the handling of linear bending angles, e.g. through the automatic addition of dummy atoms if deemed necessary by the algorithm. Additionally, Sella supports constrained optimization. Our algorithm determines the direction of the reaction coordinate through iterative diagonalization of the Hessian matrix, and does not require evaluation of the full Hessian matrix. Geometry optimization steps are chosen using the restricted step partitioned rational function optimization method, and displacements are realized using a high-performance geodesic stepping algorithm.
Hermes, E., Sargsyan, K., Najm, H. N., Zádor, J.: Accelerated saddle point refinement through full exploitation of partial Hessian diagonalization. Journal of Chemical Theory and Computation, 2019 15 6536-6549. https://doi.org/10.1021/acs.jctc.9b00869
low-temperature oxidation of cyclopentane
In this combined experimental and theoretical investigation, working with the group of my colleague, Dr. Leonid Sheps, we studied the autoignition chemistry of a prototypical cyclic hydrocarbon, cyclopentane. We used a high-pressure photolysis reactor coupled to time-resolved synchrotron VUV photoionization mass spectrometry to directly probe the short-lived radical intermediates and products, and KinBot to characterize the five PESs that are needed to explain the first- and second-O2 addition pathways. The dominant radical chain-branching pathway is ROO (+ O2) → γ-QOOH + O2 → γ-OOQOOH → products. This work paved the way for detailed comparisons with theoretical predictions from master-equation-based models for this system.
Sheps, L., Dewyer, A. L., Demireva, M., Zádor, J.: Quantitative detection of products and radical intermediates in low-temperature oxidation of cyclopentane. Journal of Physical Chemistry A, 2021 125 4467–4479. https://doi.org/10.1021/acs.jpca.1c02001
Decomposition and isomerization of 1-pentanol radicals
With my collaborators from the Ghent University, we determined stable species and saddle points on the C5H11O potential energy surface relevant for 1-pentanol pyrolysis using KinBot. We compared out predictions to flow reactor results via a kinetic model. Comparison of the simulated versus the experimental data shows that the reactions found by KinBot, for which earlier only poor estimates existed, are of significant importance to correctly describe conversion and product selectivities.
Van de Vijver, R., Van Geem, K. M., Marin, G. B., Zádor, J.: Decomposition and isomerization of 1-pentanol radicals and the pyrolysis of 1-pentanol. Combustion and Flame, 2018 196 500-514. https://doi.org/10.1016/j.combustflame.2018.05.011
Photoionization of methyl hydroperoxide
With the group of Professor Bálint Sztáray (U Pacific) and András Bődi (Paul Scherrer Institute) we studied the dissociative photoionization processes of methyl hydroperoxide (CH3OOH) using imaging Photoelectron Photoion Coincidence (iPEPICO) spectroscopy experiments and quantum-chemical and statistical rate calculations. We were able to determine a 74.2 ± 2.6 kJ mol−1 mixed experimental-theoretical 0 K heat of formation for the CH2OOH radical, the smallest QOOH radical and and the proton affinity of the Criegee intermediate, CH2OO, was also obtained to be 847.7 ± 1.1 kJ mol−1, reducing the uncertainty of the previously available computational value by a factor of 4. Extensive RRKM modeling supported by Born–Oppenheimer molecular dynamics simulations showed that the HCO+ fragment ion is produced through a roaming transition state followed by a low barrier.
Covert, K., Voronova, K., Torma, K. G., Bodi, A., Zádor, J., Sztáray, B.: Photoionization of methyl hydroperoxide: Thermochemistry of the smallest QOOH radical and the detection of a roaming fragmentation channel. Physical Chemistry Chemical Physics, 2018 20 21085-21094. https://doi.org/10.1039/C8CP03168A
Initiation reactions in acetylene pyrolysis
In gas-phase combustion systems the interest in acetylene stems largely from its role in molecular weight growth processes. The consensus is that above 1500 K acetylene pyrolysis starts mainly with the homolytic fission of the C–H bond creating an ethynyl radical and an H atom. However, below ∼1500 K this reaction is too slow to initiate the chain reaction. It has been hypothesized that instead of dissociation, self-reaction initiates this process. Nevertheless, rigorous theoretical or direct experimental evidence is lacking, to an extent that even the molecular mechanism is debated in the literature. In this work we used rigorous ab initio transition-state theory master equation methods to calculate pressure- and temperature-dependent rate coefficients for the association of two acetylene molecules and related reactions. We established the role of vinylidene, the high-energy isomer of acetylene in this process, compared our results with available experimental data, and assessed the competition between the first-order and second-order initiation steps. We also showed the effect of the rapid isomerization among the participating wells and highlighted the need for time-scale analysis when phenomenological rate coefficients are compared to observed time scales in certain experiments.
Zádor, J., Madison D. Fellows, Miller, J. A.: Initiation reactions in acetylene pyrolysis. Journal of Physical Chemistry A 2017 121 4203-4217. https://doi.org/10.1021/acs.jpca.7b03040
DIREct observation of a qooh radical
It's straightforward to write down the net combustion reaction: Oxygen reacts with hydrocarbons to form water and carbon dioxide. The details of how all the bonds break and form in succession are a great deal more complicated. Here we reported direct detection of a long-postulated piece of the puzzle, a so-called QOOH intermediate. This structure results from bound oxygen stripping a hydrogen atom from carbon, leaving a carbon-centered radical behind. We explored the influence of the hydrocarbon's unsaturation on the stability of QOOH, which has implications for both combustion and tropospheric oxidation chemistry.
Savee, J. D., Papajak, E., Rotavera, B., Huang, H., Eskola, A. J., Welz, O., Sheps, L., Taatjes, C. A., Zádor, J., Osborn, D. L.: Direct observation and kinetics of a critical reactive intermediate in hydrocarbon oxidation Science, 2015 347 643-646. https://doi.org/10.1126/science.aaa1495
reaction kinetics of qooh
Hydrocarbon autoignition has long been an area of intense fundamental chemical interest, and is a key technological process for emerging clean and efficient combustion strategies. Carbon-centered radicals containing an –OOH group, commonly denoted QOOH radicals, are produced by isomerization of the alkylperoxy radicals that are formed in the first stages of oxidation. These QOOH radicals are among the most critical species for modeling autoignition, as their reactions with O2 are responsible for chain branching below 1000 K. Despite their importance, no QOOH radicals have ever been observed by any means, and only computational and indirect experimental evidence has been available on their reactivity. Here, we directly produced a QOOH radical, 2-hydroperoxy-2-methylprop-1-yl, and experimentally determined rate coefficients for its unimolecular decomposition and its association reaction with O2. The results were supported by high-level theoretical kinetics calculations. This experimental strategy opened up a new avenue to study the chemistry of QOOH radicals in isolation.
Zádor, J., Huang, H., Welz, O., Zetterberg, J., Osborn, D.L., Taatjes, C.A.: Directly measuring reaction kinetics of QOOH – a crucial but elusive intermediate in hydrocarbon autoignition. Physical Chemistry Chemical Physics, 2013 15 10753-10760. https://doi.org/10.1039/C3CP51185E
Unconventional peroxy chemistry in alcohol oxidation
Predictive simulation for designing efficient engines requires detailed modeling of combustion chemistry, for which the possibility of unknown pathways is a continual concern. Here, we characterized a low-lying water elimination pathway from key hydroperoxyalkyl (QOOH) radicals derived from alcohols. The corresponding saddle-point structure involves the interaction of radical and zwitterionic electronic states. This interaction presents extreme difficulties for electronic structure characterizations, but we demonstrated that these properties of this saddle point can be well captured by M06-2X and CCSD(T) methods. Experimental evidence for the existence and relevance of this pathway was shown using reported data on the low-temperature oxidation of isopentanol and isobutanol. In these systems, water elimination is a major pathway, and is likely ubiquitous in low-temperature alcohol oxidation. These findings will substantially alter current alcohol oxidation mechanisms. Moreover, the methods described will be useful for the more general phenomenon of interacting radical and zwitterionic states.
Welz, O., Klippenstein, S.J., Harding, L.B., Taatjes, C.A., Zádor, J.: Unconventional peroxy chemistry in alcohol oxidation: The water elimination pathway. Journal of Physical Chemistry Letters, 2013 4 350-354. https://doi.org/10.1021/jz302004w