Activated chemistry in coupled reaction systems has broadened our understanding of the chemical kinetics. In the case of intermediates formed in gas phase abstraction reactions (e.g., OH + HC(O)C(O)H (glyoxal) →HC(O)CO + H2O), it is particularly crucial to understand how the reaction energy is partitioned between product species as this determines the propensity for a given product to undergo "prompt" dissociation (e.g., HC(O)CO → HCO + CO) before the excess reaction energy is removed. An example of such an activated system is the OH + glyoxal + O2 coupled reaction system. In this work, we develop a molecular dynamics pipeline, which, combined with a master equation analysis, accurately models previous experimental measurements. This new work resolves previous complexities and discrepancies from earlier master equation modeling for this reaction system. The detailed molecular dynamics approach employed here is a powerful new tool for modeling challenging activated reaction systems.