Ligand-Induced Electronic Response Enables Predictive QM/MM Simulations

Predictive modeling of large molecular systems demands methods that combine quantum accuracy with scalability. Although hybrid quantum mechanics/molecular mechanics (QM/MM) simulations offer such a framework, their predictive power has been limited by the subjective and system-specific definition of the QM region. Here, we present an electronically informed protocol that objectively defines QM regions from ligand-induced orbital shifts and charge-redistribution, extracted in a single semiempirical fragment molecular orbital (FMO) calculation. Validated on both zeolite-guest and enzyme-inhibitor complexes, the method achieves chemical accuracy (within ∼1-2 kcal/mol on binding energies) while substantially reducing computational cost at the DFTB level. This cross-domain strategy reframes QM/MM as a transferable design principle, bridging solid-state catalysis and quantum biochemistry, and thereby providing a practical platform for predictive molecular engineering across diverse disciplines.