@article{JuhaszSerraLakatosetal.2023, author = {Juhasz, Anett and Serra, Uneri Haymana and Lakatos, Csilla and Vadkerti, Bence and Ragyanszki, Anita and Farkas, Odon and Keki, Sandor and Nagy, Lajos}, title = {The kinetics of uncatalyzed and catalyzed urethane forming reactions of aliphatic diisocyanates with butan-1-ol}, volume = {47}, journal = {New J. Chem.}, doi = {10.1039/d3nj02747c}, pages = {16096 -- 16107}, year = {2023}, abstract = {The kinetics of the urethane forming reactions of hexamethylene diisocyanate (HDI), 4,4′-dicyclohexyl-methane-diisocyanate (HMDI) and isophorone diisocyanate (IPDI) with butan-1-ol were systematically studied by electrospray ionization mass spectrometry (ESI-MS) in the off-line mode. The reactions were performed in toluene solution in the temperature range of 50-80 °C and perdeuterated butan-1-ol was used for quenching the reaction. The butan-1-ol was employed in high excess to diisocyanates to obtain pseudo first-order rate coefficients. For rendering the kinetics, a simple A → B → C consecutive model was applied and found to adequately describe the observed kinetic behaviors. The corresponding rate coefficients were determined and reactivities of the diisocyanates were found to decrease in the order HDI > IPDI > HMDI. Furthermore, it was observed that the second isocyanate group in HDI, due to the ring formation by intramolecular hydrogen bonds, reacted faster with butan-1-ol after the first isocyanate moiety had reacted. The formation of hydrogen bonding rings was also confirmed by DFT calculations. However, the reactivity of the second isocyanate moiety (after the first one has reacted) did not change significantly in the case of HMDI. From the temperature dependences the apparent activation parameters such as the pre-exponential factors and activation energies were determined. In addition, the reactions were also studied at 80 °C in the presence of tin(II)-2-ethylhexanoate at different concentrations and a mechanism was proposed for the catalytic process.}, language = {en} } @article{JiRagyanszkiFournier2023, author = {Ji, Hongchen and Ragyanszki, Anita and Fournier, Rene A.}, title = {Machine learning estimation of reaction energy barriers}, volume = {1229}, journal = {Computational and Theoretical Chemistry}, doi = {10.1016/j.comptc.2023.114332}, pages = {114332}, year = {2023}, abstract = {We describe a machine learning approach to approximate reaction energy barriers (E), requiring as input only estimates of geometry and energies of reactants and products. Using the dataset of Grambow, Pattanaik, and Green [Sci. Data 7 (1 3 7) (2020)] for reactions involving seven or fewer non-hydrogen atoms, 300 reaction features are computed, and an estimate of E is obtained by fitting a Kernel Ridge Regression (KRR) model with Laplacian kernel to a subset of Density Functional Theory reaction barriers. Our main interest is small energy barriers with the goal of modeling reactions in the interstellar medium and circumstellar envelope. We omitted reactions with E > 40 kcal mol-1 to obtain a subset of 5,276 reactions for 5-fold cross-validation. For this set, the KRR model predicts E with a mean absolute error of 4.13 kcal mol-1 and a root-mean square error of 6.02 kcal mol-1.}, language = {en} } @misc{RagyanszkiJiFournier2024, author = {Ragyanszki, Anita and Ji, Hongchen and Fournier, Rene}, title = {Understanding the Origins of Life - A Machine learning approach to estimate reaction mechanisms of biotic precursors}, journal = {Perspectives and challenges of future HPC installations for atomistic and molecular simulations}, year = {2024}, abstract = {Life as we know it is the result of billions of years of evolution; yet, understanding how the very first organisms came into existence is a challenge that has yet to be solved. One theory states that components of the first biotic molecules may not have formed on Earth. Rather, they may have initially formed in the interstellar medium (ISM) and been transported to Earth, as supported by recorded instances of organic molecules detected in space. The ISM, with its low temperatures and specific collision processes, allows for molecular stability and the formation of biotic precursors that would otherwise be unlikely in Earth's prebiotic conditions. Understanding how these molecules formed in the ISM may be the key to determining how life began. The goal of this research is to develop a new model for solving astrobiophysical problems by studying the formation mechanisms of biomolecules found in the ISM. Although such pathways have been studied individually, there has not yet been a comprehensive method to understand all the formation reactions that can occur in ISM. Several quantum chemical and numerical methods are available for finding transition states (TS) and energy barriers (E) of chemical reactions but are time-consuming and can hardly be applied to systems with more than a few atoms. Our main interest is to develop a a machine learning approach to approximate TS, and E, requiring as input only estimates of geometry and energies of reactants and products. Using a complete dataset 300 reaction features are computed, and an estimate of E is obtained by fitting a Kernel Ridge Regression (KRR) model with Laplacian kernel, and a fully connected Artificial Neural Network (ANN) to estimate reaction energy barriers.}, language = {en} } @misc{RagyanszkiJiFournier2024, author = {Ragyanszki, Anita and Ji, Hongchen and Fournier, Rene}, title = {Understanding the Origins of Life - A Machine learning approach to estimate reaction mechanisms of biotic precursors}, journal = {SIMPLAIX}, year = {2024}, abstract = {Understanding the Origins of Life - A Machine learning approach to estimate reaction mechanisms of biotic precursors. Life as we know it is the result of billions of years of evolution; however, understanding how the very first organisms came into existence is a challenge that has yet to be solved. One theory states that components of these molecules may have formed in the interstellar medium (ISM) and been transported to Earth. The ISM, with its specific conditions, allows for molecular stability and the formation of biotic precursors that would otherwise be unlikely in Earth's prebiotic conditions. Understanding how these molecules formed in the ISM may be the key to determining how life began. The goal of this research is to develop a model for solving astrobiophysical problems by studying the formation mechanisms of biomolecules found in the ISM. Although such pathways have been studied individually, there has not yet been a comprehensive method to understand the complete reactions mechanisms. Several QM methods are available for finding transition states (TS) and energy barriers (E) of chemical reactions but are time-consuming and can hardly be applied to more complex systems. Our interest is to develop a machine learning approach to approximate TS, and E, requiring as input only estimates of geometry and energies of reactants and products.}, language = {en} } @article{JiRagyanszkiFournier2024, author = {Ji, Hongchen and Ragyanszki, Anita and Fournier, Rene}, title = {A Machine Learning and Quantum Chemistry Approach for Identifying Prebiotic Molecules in the Interstellar Medium}, journal = {Physical Chemistry Chemical Physics}, year = {2024}, abstract = {The discovery of molecules in the interstellar medium (ISM) plays a key role in understanding prebiotic chemistry. Relatively few (∼250) molecules have been confirmed in the ISM, and detecting additional species is crucial for expanding our knowledge of astrochemical processes. We present a strategy for predicting possible prebiotic molecules in the ISM that combines machine learning and high-accuracy quantum chemistry calculations. Using a reaction dataset of over 153,000 possible combinations of known interstellar molecules, we applied a machine learning model to estimate reaction energy barriers and identify those with low or zero barriers that are most likely to occur in the ISM. From this screening process, 24 molecules were identified, five of which have already been observed in interstellar space. For the remaining 19 molecules, we conducted density functional theory (DFT) and coupled cluster theory calculations to determine the most stable conformers, spectroscopic parameters, and predict their detectability through spectroscopy. We present data to guide future observational searches for new interstellar species, contributing to the ongoing exploration of complex organic molecules in space and their potential role in prebiotic chemistry.}, language = {en} } @article{RozsaRagyanszkiViskolczetal.2023, author = {Rozsa, Zsofia Borbala and Ragyanszki, Anita and Viskolcz, Bela and Szori, Milan}, title = {Chemical space of the singlet C4H8O2 species. A systematic theoretical analysis on their structural and thermochemical properties}, volume = {1225}, journal = {Computational and Theoretical Chemistry}, doi = {10.1016/j.comptc.2023.114162}, pages = {114162}, year = {2023}, abstract = {The goal of this study was to explore and define the thermodynamic properties of one of the subspaces of 'chemical space' using a mixture of graph theory and theoretical chemistry tools. Therefore, all possible mo- lecular structures with C4H8O2 stoichiometry were generated, considering constitutional isomers and molecular complexes. The thermodynamic properties of the obtained isomers have been obtained by G3MP2B3 protocol. The classification of the obtained isomers was simplified by using thermodynamic maps, which is an effective method for the comparison of thermodynamic stability for entities of complex molecular systems. Modern computational methods can be used to understand larger systems, which has made it possible to characterize a chemical subspace not only by selecting individual entities, but also as a whole. With this pro- cedure one can catch a glimpse into the diversity of a molecular system and predict further uses of newly discovered molecules or design molecules with predefined properties.}, language = {en} } @article{RagyanszkiFiserLeeRuffetal.2023, author = {Ragyanszki, Anita and Fiser, Bela and Lee-Ruff, Edward and Liebman, Joel F.}, title = {Strained Small Nitrogen Heterocycles-Azabicyclobutanes and Azirines}, volume = {8}, journal = {ChemistrySelect}, number = {26}, doi = {10.1002/slct.202301405}, pages = {e202301405}, year = {2023}, abstract = {Small ring nitrogen heterocycles, azabicyclobutanes and azirines, were investigated by computational methods in order to address the discrepancy between their regioisomers 1- and 2-azabicyclobutane and 1H- and 2H-azirines. Both 1-azabicyclobutane and 2H-azirine are well known synthetic starting points to larger nitrogen heterocycles whereas 2-azabicyclobutane and 1H-azirine and their derivatives have yet to be reported as isolable compounds. Calculated parameters such as structure, base strength (proton affinities), NICS values and enthalpies of formation from which strain energies are derived are reported. The destabilization of the less stable regioisomers is attributed to homoantiaromaticity in 2-azabicyclobutane and antiaromaticity in 1H-azirine. Two stereoisomers exist for 2-azabicyclobutane with the endo- stereoisomer being more stable. This phenomenon is indicative of the hydrogen bond acceptor properties of the neighboring cyclpropane and the π-bond character of the central bond in 2-azabicyclobutane.}, language = {en} } @article{LamboKoyanagiRagyanszkietal.2023, author = {Lambo, Ricardo Lewis and Koyanagi, Gregory K. and Ragyanszki, Anita and Horbatsch, Marko and Fournier, Rene and Hessels, Eric A.}, title = {Calculation of the local environment of a barium monofluoride molecule in an argon matrix: a step towards using matrix-isolated BaF for determining the electron electric dipole moment}, volume = {121}, journal = {Molecular Physics}, number = {6}, doi = {10.1080/00268976.2023.2198044}, year = {2023}, language = {en} } @article{KoyanagiLamboRagyanszkietal.2023, author = {Koyanagi, Gregory K. and Lambo, Ricardo Lewis and Ragyanszki, Anita and Fournier, Rene A. and Horbatsch, Marko W. and Hessels, Eric A.}, title = {Accurate calculation of the interaction of a barium monofluoride molecule with an argon atom: A step towards using matrix isolation of BaF for determining the electron electric dipole moment}, volume = {391}, journal = {Journal of Molecular Spectroscopy}, doi = {10.1016/j.jms.2023.111736}, pages = {111736}, year = {2023}, language = {en} } @article{JiAnitaFournier2025, author = {Ji, Hongchen and Anita, Ragyanszki and Fournier, Rene}, title = {Computational Study of the Reactions of CH2 with HCNO and HNCO}, volume = {103}, journal = {Canadian Journal of Chemistry}, number = {7}, doi = {10.1139/cjc-2024-0203}, pages = {386 -- 395}, year = {2025}, abstract = {We present a computational approach for screening reaction mechanisms with machine learning estimates of energy barriers. A comprehensive screening of thousands of reactions identified the CH2 reactions with HCNO and HNCO as possible sources of relatively complex organic molecules in space. We report detailed reaction mechanisms, including TS, intermediate, and product energies, calculated with density functional theory and coupled cluster theory. Singlet CH2, located 9 kcal/mol above the triplet ground state, reacts with HCNO or HNCO without a barrier, producing four prod11 ucts: CH2NCHO, N-methyleneformamide, the thermodynamically favored product; NHCHCHO, imine acetaldehyde; NHCHOCH; and (CH2OC)NH, oxiran-2-ylazanide. The lowest energy pathway for CH2 + HCNO, involving a triplet-to-singlet crossing, has a barrier of 8 kcal/mol and leads to N -methyleneformamide, imine acetaldehyde, and NHCHOCH. The reaction of triplet CH2 with HNCO has a lowest energy pathway with a barrier of 11 kcal/mol, yielding CH2(CO)NH.}, language = {en} }