On the Importance of Lennard–Jones Parameter Calibration in QM/MM Framework: Reaction Path Tracing via Free Energy Gradient Method for Ammonia Ionization Process in Aqueous Solution

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<jats:title>Abstract</jats:title> <jats:p>The free energy gradient (FEG) method combined with the QM/MM–MD calculation has realized full-atomic structural optimization of the solute NH3–H2O molecule pair in aqueous solution, exploring successful tracing of the reaction path on the free energy surface from the neutral state (H3N–H2O) to the ionized (H4+N–O−H) through the transition state (H3N···H+···O−H). To reproduce accurately the structural change of the hydrated molecule pair, the LJ parameter calibration in the QM/MM nonelectrostatic interaction was essential for four kinds of QM solute species, i.e., OH−, H2O, NH3, and NH4+, treated in the NDDO-SSRP framework with the ab initio quality. Two linear interpolations of these calibrated LJ parameters optimized at the NSS and ISS were utilized in the path-dependent FEG calculation, as is common in the free energy perturbation treatment. After including the effects of the intramolecular entropic contribution and quantum tunneling, the free energies of activation and reaction were satisfactorily estimated to be 13.8 and 9.8 kcal mol−1 (1 kcal = 4.184 kJ), respectively. It is expected that far more agreement with the experimental values should be reasonably attained if the QM region were extended to three surrounding water molecules to take in the electron delocalization effect adequately.</jats:p>

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