Propyl phosphonic acid cyclic anhydride (T3P)-mediated peptide coupling reactions are widely used in small molecule synthesis and Active Pharmaceutical Ingredient (API) scale-ups. Leveraging powerful process analytical tools—in-situ FTIR, NMR, and HPLC—in combination with kinetic modeling, and Density Functional Theory (DFT) calculations allowed us to investigate the underlying coupling mechanism between various carboxylic acids and secondary amines mediated by T3P and N,N-Diisopropylethylamine (DIPEA). This synergistic approach not only revealed an intriguing multi-step mechanism for acid activation and acylation but also enabled kinetic modeling of extremely rapid elementary steps. The proposed mechanism helped establish optimal strategies for the reagent addition sequence, equivalents, and reaction time to maximize the overall yield of the process. The resulting calibrated kinetic model serves as a foundation for a systems model enabling design and control of continuous synthesis processes for a proprietary API from Sanofi's small molecule portfolio.
