QM/MM(ABEEM) Study on the Ligand Substitution Processes of Ruthenium(III) Complex NAMI‐A

Abstract

QM combined with ABEEMσπ (atom-bond electronegativity equalization method) fluctuating charge polarizable force field [QM/MM(ABEEM)] has been employed to investigate the hydrolysis mechanism of ruthenium(III) complex NAMI-A. Eleven possible hydrolysis paths of NAMI-A and its hydrolysates have been unveiled. Structures obtained by QM/MM (ABEEM) method were used to calculate the activation free energy by free energy perturbation theory. Based on analysis of structures and activation free energies, it is found that the rate of DMSO dissociation is faster than that of Cl  dissociation in the first step, which is in agreement with experimental results. Hydrolysates of the first step continue to hydrolyze with lower activation free energies than that of the first hydrolysis step, but the trans-position Cl  hydrolysis in the second step needs more time to perform. This can account for experimental phenomenon reasonably. We have simulated further hydrolysis paths of the hydrolysates, then found that both Cl  dissociation and DMSO dissociation take place in the third hydrolysis step and [RuCl(H 2 O) 4 (Im)] 2＋ is the main solute in aqueous solution after the fourth hydrolysis step.Keywords computational chemistry, reaction mechanisms, QM/MM(ABEEM), ABEEMσπ polarizable force field, activation free energy QM/MM(ABEEM) Study on the Ligand Substitution Processes of Ruthenium(III) ComplexChin.

Reaction mechanism of NO with hydrolysates of NAMI‐A: an MD simulation by combining the QM/MM(ABEEM) with the MD‐FEP method

“…Wilson and Ichikawa and Torrent‐Sucarrat and coworkers pointed out that the charge transfer between atoms in a molecule is overestimated by using the polarization basis sets. Huzinaka et al, Jakalian et al, Watanabe et al, and our group have shown that the use of higher levels of basis sets overestimates the overlap between their respective basis functions belonging to two atoms in a molecule. Bayly and his coworkers pointed out that when the 6‐31G* basis set is used, the polarity of a molecule calculated by the partial charges is overestimated by 10%–15% .…”

“…To take the effect of aqueous solution into account, activation free energies were computed by using the combined QM/MM(ABEEM) and free energy perturbation (FEP) theory . The detailed description of the QM/MM(ABEEM) method and free energy perturbation theory can be found in our previous articles, and some ABEEMσπ parameters of ruthenium complexes were determined by our previous work, while others were calibrated and determined through a regression and least‐squares optimization procedure. The details were described in our previous articles .…”

“…The detailed description of the QM/MM(ABEEM) method and free energy perturbation theory can be found in our previous articles, and some ABEEMσπ parameters of ruthenium complexes were determined by our previous work, while others were calibrated and determined through a regression and least‐squares optimization procedure. The details were described in our previous articles . All ABEEMσπ parameters are listed in Supporting Information Table S1.…”

“…This step is ascribed to the hydrolysis reactions being able to open up a coordination site before target molecule coordination to the Ruthenium center of NAMI‐A . In our previous work, we have employed the combined QM and ABEEM polarizable force field [Quantum Mechanics (QM)/Molecular Mechanics (MM)(ABEEM)] method to investigate the serial hydrolysis reactions of NAMI‐A . In this article, we have used the first‐ and second‐step hydrolysates of NAMI‐A as model molecules to investigate the mechanisms of H 2 O‐NO ligand exchange reaction.…”

“…To simulate the solvent, the explicit solvent model described by an ABEEMσπ polarizable force field with the ABEEM‐7P water model has been used . Activation free energy is calculated by QM/MM(ABEEM) combined with molecular dynamics‐free energy perturbation (MD‐FEP) calculation. The activation free energies of the H 2 O‐NO ligand exchange reactions for various hydrolysates of NAMI‐A are compared.…”