Planar vs. Twisted Pyrimidine Derivatives: Insights from Molecular Dynamics and Predictive Modelling for Melamine Detection in Dairy Products

Abstract

Herein, we report the design and synthesis of two pyrimidine derivatives with different donor substituents Pyrene (1) and Anthracene (2) that show aggregation in the aqueous medium. The aggregates of compound 1 were found to be pH-sensitive as well as thermoresponsive. The energy-optimized structure of compound 1 revealed a nearly planar conformation with a dihedral angle of ~0.2° between the donor and the acceptor moieties, which appeared to be ~50.8° for compound 2. A 2.5-fold and 5-fold turn-on response was observed after the addition of melamine for compounds 1 and 2 respectively. MD simulations were employed to analyze the stability, interaction energies, and aggregation tendencies of the compounds. The self-assembled structures of 1 after 120 ns showed anti-parallel arrangement with pyrene moiety of one molecule π-stacked with pyrimidine unit of another molecule. On the contrary, in the case of compound 2, anthracene moieties were involved in face-to-face π-stacking interaction, while multiple hydrogen bonds (1.8 – 2.2 A°) were observed among pyrimidine residues. Also, various machine learning models have been utilized to predict the normalized intensity of melamine based on concentration vs intensity data. The linear regression model (R2 = 0.9959) stands out with the best performance metrics, reinforcing that a linear approach is highly effective for predicting normalized intensity based on concentration in this dataset. Furthermore, compound 1 was employed for the estimation of melamine content in milk products, and the results were successfully validated using alternative analytical methods (LCMS). Furthermore, accurate quantification of melamine levels in the milk samples was achieved (LOD 0.8 ppm). It was also noted that chemically modified paper strips were capable of detecting melamine in adulterated milk samples without the need for any advanced instrumentation.