Metal ions play fundamental roles in geochemistry, biochemistry and materials science.With the tremendous increasing power of the computational resources and largelyinventions of the computational tools, computational chemistry became a more and moreimportant tool to study various chemical processes. Force field modeling strategy, whichis built on physical background, offered a fast way to study chemical systems at atomiclevel. It could offer considerable accuracy when combined with the Monte Carlo orMolecular Dynamics simulation protocol. However, there are various metal ions and it isstill challenging to model them using available force field models. Generally there areseveral models available for modeling metal ions using the force field approach such asthe nonbonded model, the bonded model, the cationic dummy atom model, the combinedmodel, and the polarizable models. Our work concentrated on the nonbonded and bondedmodels, which are widely used nowadays. Firstly, we focused on filling in the blanks ofthis field. We proposed a noble gas curve, which was used to describe the relationshipbetween the van der Waals radius and well depth parameters in the 12-6 Lennard-Jonespotential. By using the noble gas curve and multiple target values (the hydration freeenergy, ion-oxygen distance, coordination number values), we have consistentlyparameterized the 12-6 Lennard-Jones nonbonded model for 63 different ions (including11 monovalent cations, 4 monovalent anions, 24 divalent cations, 18 trivalent cations,and 6 tetravalent cations) combined with three widely used water models (TIP3P, SPC/E, and TIP4PEW). Secondly, we found there is limited accuracy of the 12-6 model, whichmakes it hard to simulate different properties simultaneously for ions with formal chargeequal or larger than +2. By considering the physical origins of the 12-6 model, weproposed a new nonbonded model, named the 12-6-4 LJ-type nonbonded model. Wehave systematically parameterized the 12-6-4 model for 55 different ions (including 11monovalent cations, 4 monovalent anions, 16 divalent cations, 18 trivalent cations, and 6tetravalent cations) in the three water models. It was shown that the 12-6-4 model couldreproduce several properties at the same time, showing remarkable improvement over the12-6 model. Meanwhile, through the usage of a proposed combining rule, the 12-6-4model showed excellent transferability to mixed systems. Thirdly, we have developed theMCPB.py program to facilitate building of the bonded model for metal ion containingsystems, which can largely reduce human efforts. Finally, an application case of ametallochaperone - CusF was shown, and based on the simulations we hypothesized anion transfer mechanism.
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