Site- and conformer-specific reaction dynamics of glycine with the hydroxyl radical

Understanding the state-to-state atomic-level dynamics of a chemical reaction is a central topic in modern chemistry. Moving beyond the traditional mode-specific reaction dynamics studies, here we investigate the concept of site and conformer specificity by studying the reaction of the glycine molecule (H₂NCH₂COOH) with the hydroxyl (OH) radical using first-principles theory. Conformer-specific quasi-classical trajectory computations on a 30-dimensional potential energy surface reveal three distinct H-abstraction pathways targeting the different functional groups. CH₂- and NH₂-H-abstraction proceed through direct, single-step mechanisms, whereas a two-step mechanism emerges for COOH-H-abstraction, where initial dehydrogenation frequently leads to fragmentation into CO₂ and CH₂NH₂. COOH-H-abstraction is favored at low energies, while NH₂- and CH₂-H-abstraction are promoted at higher energies. The formation of the unstable H₂NCH₂COO• intermediate becomes increasingly restricted at higher collision energies due to limited interaction time. In specific reactant conformers, the simulations reveal an indirect biradical mechanism and an alternative stabilization pathway via intramolecular H transfer. Product-conformer distributions exhibit a three-step pattern of carboxyl group rearrangement-H-orientation switch, 180° rotation around the C-C axis, and their combination-during NH₂- and CH₂-H-abstraction. Structure-specific product formation arises clearly only in CH₂-H-abstraction, driven by the closed COOH conformation, whereas NH₂-H-abstraction leads to conformational diversity in the products.