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Computational elucidation of the reaction mechanism for synthesis of pyrrolidinedione derivatives via Nef-type rearrangement - cyclization reaction.

ABSTRACT: This paper reports a quantum chemical study of all stages of a one-pot synthesis of pyrrolidinedione derivatives from nitromethane and coumarin, which includes Michael addition, migration of an oxygen atom (Nef-type rearrangement), and cyclization to a pyrrolidine ring. The energy barrier of deprotonated nitromethane addition to coumarin is 21.7 kJ mol^-1, while the barrier of proton transfer from the methylene to the nitro group in the nitromethyl group is notably higher, 197.8 kJ mol^-1. The second stage of the reaction, migration of an oxygen atom within the nitromethyl group, occurs with lowest energy barrier, 142.4 kJ mol^-1, when it is assisted by an additional water molecule. The last stage - cyclization, passes with a very low energy barrier of 11.9 kJ mol^-1 but the tautomerization of the nitrosohydroxymethyl group to the hydroxy-N-hydroxyiminomethyl, necessary for the process, has an energy barrier of 178.4 kJ mol^-1. Analogous calculations for the same process with the ethyl ester of 3-coumarin-carboxylic acid as substrate show that the relative energies of the intermediates and transition states are by at most 10-16 kJ mol^-1 more stable than the corresponding structures with coumarin.

SUBMITTER: Ilieva ED

PROVIDER: S-EPMC9077586 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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Computational elucidation of the reaction mechanism for synthesis of pyrrolidinedione derivatives <i>via</i> Nef-type rearrangement - cyclization reaction.

Ilieva Eleonora D ED Petrova Galina P GP Nikolova Rositca D RD Vayssilov Georgi N GN

RSC advances 20180116 6

This paper reports a quantum chemical study of all stages of a one-pot synthesis of pyrrolidinedione derivatives from nitromethane and coumarin, which includes Michael addition, migration of an oxygen atom (Nef-type rearrangement), and cyclization to a pyrrolidine ring. The energy barrier of deprotonated nitromethane addition to coumarin is 21.7 kJ mol<sup>-1</sup>, while the barrier of proton transfer from the methylene to the nitro group in the nitromethyl group is notably higher, 197.8 kJ mol ...[more]

PMID: 35541181

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Project description:Compound identification from accurate mass MS/MS spectra is a bottleneck for untargeted metabolomics. In this study, we propose nine rules of hydrogen rearrangement (HR) during bond cleavages in low-energy collision-induced dissociation (CID). These rules are based on the classic even-electron rule and cover heteroatoms and multistage fragmentation. We evaluated our HR rules by the statistics of MassBank MS/MS spectra in addition to enthalpy calculations, yielding three levels of computational MS/MS annotation: "resolved" (regular HR behavior following HR rules), "semiresolved" (irregular HR behavior), and "formula-assigned" (lacking structure assignment). With this nomenclature, 78.4% of a total of 18506 MS/MS fragment ions in the MassBank database and 84.8% of a total of 36370 MS/MS fragment ions in the GNPS database were (semi-) resolved by predicted bond cleavages. We also introduce the MS-FINDER software for structure elucidation. Molecular formulas of precursor ions are determined from accurate mass, isotope ratio, and product ion information. All isomer structures of the predicted formula are retrieved from metabolome databases, and MS/MS fragmentations are predicted in silico. The structures are ranked by a combined weighting score considering bond dissociation energies, mass accuracies, fragment linkages, and, most importantly, nine HR rules. The program was validated by its ability to correctly calculate molecular formulas with 98.0% accuracy for 5063 MassBank MS/MS records and to yield the correct structural isomer with 82.1% accuracy within the top-3 candidates. In a test with 936 manually identified spectra from an untargeted HILIC-QTOF MS data set of human plasma, formulas were correctly predicted in 90.4% of the cases, and the correct isomer structure was retrieved at 80.4% probability within the top-3 candidates, including for compounds that were absent in mass spectral libraries. The MS-FINDER software is freely available at http://prime.psc.riken.jp/ .

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Computational elucidation of the reaction mechanism for synthesis of pyrrolidinedione derivatives via Nef-type rearrangement - cyclization reaction.

Publications

Computational elucidation of the reaction mechanism for synthesis of pyrrolidinedione derivatives <i>via</i> Nef-type rearrangement - cyclization reaction.

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