The development of environmentally friendly synthetic methodologies is a central and urgent goal of modern chemical science and industry. Advancing mechanistic understanding is crucial to accelerating the development of new reactions involving biobased platform molecules which can be applied to sustainable process design. The ab initio nanoreactor is a method for automated generation of mechanistic trajectories, in which high temperatures, high pressures, and external forces are applied to assemblies of reactants to advance discovery using first-principles MD simulations. I used this ab initio nanoreactor method to solve mechanistic mysteries of green and biological chemistry, which has proved pivotal in a synergistic theoretical and experimental studies. In another application, reaction design and accurate predictions of ligand-protein/protein-protein binding energies is critical in pharmaceutical drug development, and can drive efficient production from predicted reagents, minimize waste, and elucidate the core organizations of biology. Many disease-causing viruses target sialic acids (Sias) on the surface of host cells. Some viruses bind preferentially to sialic acids with O-acetyl modification at the hydroxyl group of C7, C8, or C9 on the glycerol-like side chain. Binding studies of proteins to sialosides containing O-acetylated sialic acids are crucial in understanding the related diseases, but experimentally difficult due to the lability of the ester group. As such, N-acetyl sialic acids have been proposed as stable mimics. I have studied the instability of the ester group across modified Sias, and the structural and biological similarities of these Sias in ligand-protein binding with MERS-CoV S and SARS-CoV-2 S proteins. I have found N-acetyl and O-acetyl Sias interchangeable, suggesting an experimentally reasonable mimic to probe viral mechanisms.