Mechanisms of Plasma-Induced Oxidative Degradation of L-Proline and trans-4-Hydroxy-L-proline: A Computational Study

Abstract Cold atmospheric plasma (CAP) has emerged as a convenient tool for modifying biomolecules, including amino acids, through the generation of reactive oxygen and nitrogen species. The impact of these species on biological molecules is a central question in biochemistry and biomedicine. In this study, we employed molecular dynamics (MD) simulations, utilizing the density functional tight-binding (DFTB) potential, and density functional theory (DFT) calculations to investigate the dynamic evolution of two amino acids, L-proline and trans-4-hydroxy-L-proline, in the presence of oxygen radicals. The species and mechanisms were investigated both in the gas phase and aqueous solution. DFTB-MD simulations provided mechanistic insights into the chemical modifications observed experimentally. The simulations revealed that L-proline undergoes significant structural changes, including ring opening, fragmentation, and the formation of new functional groups (e.g., –OH, C=O), whereas trans-4-hydroxy-L-proline exhibits greater resistance to these modifications due to the stabilizing effect of the hydroxyl group. Vibrational spectra of the pristine and modified amino acids were also simulated using DFT and compared with literature data. These findings contribute to a deeper understanding of plasma-induced amino acid modifications, supporting the advancement of plasma-based biomedical applications.

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