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 

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 

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

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. D., Sagsyan, K., Najm, H. N., Zádor, J.: Sella, an open-source automation-friendly molecular saddle point optimizer. Journal of Chemical Theory and Computation, 2022 18 6974–6988. https://pubs.acs.org/doi/10.1021/acs.jctc.2c00395

Hermes, E. D., Sagsyan, K., Najm, H. N., Zádor, J.: A geodesic approach to internal coordinate optimization. The Journal of Chemical Physics, 2021 155 094105. https://doi.org/10.1063/5.0060146

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

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

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

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