Biomimetic Fermentation Reshapes Precursor Pools to Drive Synergistic Roasting Reactions and Enhance Coffee Flavor Complexity

Deciphering the coupling mechanisms between post-harvest precursor shaping and roasting thermochemistry is pivotal for precise coffee flavor modulation. This study aimed to investigate the regulation mechanisms of in vitro biomimetic fermentation (BF) on the precursor-roasting reaction network. Integrated multi-omics characterization and sensory evaluation reveal that the BF protocol achieves targeted substrate enrichment, notably amplifying free amino acids—particularly leucine and phenylalanine—by 1.89-fold while accumulating lactate and succinate buffering salt systems. This reconfiguration constructs a matrix with superior thermal buffering capacity (ΔpH 0.17), which optimizes the thermal reaction kinetic window during roasting. Consequently, BF drives a 3.08-fold surge in esterification flux, significantly increasing the abundance of key fruity markers such as ethyl acetate and ethyl isovalerate. It also enhances the diversity of Maillard products, specifically elevating nutty-associated alkylpyrazines (e.g., 2,3,5-trimethylpyrazine). Concurrently, BF improves the thermal stability of bioactive compounds, including 5-caffeoylquinic acid (5-CQA) and trigonelline. Multi-scale molecular dynamics and quantum chemical calculations elucidate that BF-derived organic acid–salt complexes exert a ‘pseudo-catalytic effect,’ lowering activation free energy barriers for critical aroma-generating reactions by approximately 8.5 kcal/mol. This study demonstrates high sensory predictability (predictive model R2 = 0.98) and provides a quantitative theoretical framework to advance coffee processing from empirical observation to rational flavor design.