Binding Free Energies of Divalent Cations to Functional Groups of Amino Acids with OPLS-AA Force Field
Abstract
Purification of water from heavy metal ions is an urgent environmental problem. An actively studied method for this is the binding of metal ions by means of natural materials like plant proteins, as well as engineered materials like functionalized carbon allotropes. Carboxyl, thiol, amino groups are capable of complexing with metal cations, which leads to the removal of pollutants from water. Computational chemistry methods including classical molecular dynamics modeling are actively used in search of suitable materials. The paper evaluates the correctness of reproducing binding free energies of a number of divalent metal cations with functional groups found in amino acids using OPLS-AA force field. Both standard built-in and recently used potential models of cations are considered. Comparisons are made with respect to experimentally measured stability constants of modeled complexes or their structural analogues. Calculations of free energies are performed by the method of alchemical transformation. It is shown that despite the validity of the potential models, the binding free energies to functional groups of amino acids are generally poorly reproduced: strongly overestimated for the carboxylate group, underestimated for the thiolate and amino groups, and incorrect for imidazole. This indicates that OPLS-AA force field should be used with caution for calculation of the energy characteristics of metal binding. The way to fix potential models in order to accurately reproduce experimental values is outlined and applied to four cation – ligand complexes.
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