Benchtop ¹⁹F Nuclear Magnetic Resonance (NMR) Spectroscopy Provides Mechanistic Insight into the Biginelli Condensation toward the Chemical Synthesis of Novel Trifluorinated Dihydro- and Tetrahydropyrimidinones as Antiproliferative Agents

Abstract

Benchtop nuclear magnetic resonance (NMR) spectroscopy has enabled the monitoring and optimization of chemical transformations while simultaneously providing kinetic, mechanistic, and structural insight into reaction pathways with quantitative precision. Moreover, benchtop NMR proton lock capabilities further allow for rapid and convenient monitoring of various organic reactions in real time, as the use of deuterated solvents is not required. The complementary role of 19F NMR-based kinetic monitoring in the fluorination of bioactive compounds has many benefits in the drug discovery process since fluorinated motifs additionally improve drug pharmacology. In this study, 19F NMR spectroscopy was utilized to monitor the synthesis of novel trifluorinated analogs of monastrol, a small molecule dihydropyrimidinone kinesin-Eg5 inhibitor, and to probe the mechanism of the Biginelli cyclocondensation, a multicomponent reaction used to synthesize dihydropyrimidinone and tetrahydropyrimidinones through a Bronsted- or Lewis-acid catalyzed cyclocondensation between ethyl acetoacetate, thiourea, and an aryl aldehyde. In the present study, a trifluorinated ketoester serves a dual purpose as being the source of the trifluoromethyl group in our fluorinated dihydropyrimidinones and as a spectroscopic handle for real-time reaction monitoring and tracking of reactive intermediates by 19F NMR. Further, upon extending this workflow to a diverse array of 3- and 4-substituted aryl aldehydes, we were able to derive Hammett linear free energy relationships (LFER) to determine stereoelectronic effects of para- and meta-substituted aryl aldehydes to corresponding reaction rates and mechanistic routes. In addition, we used density functional theory (DFT) calculations to corroborate our experimental results through the thermodynamic values of key intermediates in each mechanism. Finally, these studies culminate in the synthesis of a novel trifluorinated analog of monastrol and its subsequent biological evaluation in vitro. More broadly, we show an application of benchtop 19F NMR spectroscopy as an analytical tool in the real-time investigation of a mechanistically and chemically complex multicomponent reaction mixture.

Trifluoromethyl‐β‐dicarbonyls as Versatile Synthons in Synthesis of Heterocycles

“…Very recently, Chen et al reported the synthesis of a diverse library of trifluoromethylated tetrahydropyrimidinone derivatives 412' via a one-pot three-component reaction of ethyl 4,4,4-trifluoro-3-oxobutanoate 1, thiourea 221, and para-and meta-substituted aryl aldehydes 138 in the presence of ytterbium(III) triflate catalyst in acetonitrile (Scheme 141). [239] Authors utilized benchtop 19 F NMR spectroscopy to probe the mechanism of the Biginelli cyclocondensation and the obtained results showed that the reaction follows the enamine mechanism, involving initial condensation of thiourea and β-ketoester.…”

Perspectives on Nuclear Magnetic Resonance Spectroscopy in Drug Discovery Research

“…The crude reaction mixtures were directly analyzed by 19 F NMR. Reproduced with permission from ref . Copyright 2023 American Chemical Society.…”

“…They have found uses for reaction monitoring, chemical analysis, and quantification and analysis of metabolite profiles among others. An inspection of recently published articles shows benchtop NMR data contributing to the quantification of oxidation products, 123 mechanistic insights of synthetic reactions (Figure 33), 124 cycloaddition reaction monitoring, 125 and complex biofluid mixture analysis. 126 Throughout this perspective, we see that numerous NMR workflows are underpinned by computational methods to accelerate data analysis.…”