Abstract
The coordination of Pb(II) in aqueous solutions containing thiols is a pivotal topic to the understanding of the pollutant potential of this cation. Based on its hard/soft borderline nature, Pb(II) forms stable hydrated ions as well as stable complexes with the thiol groups of proteins. In this paper, the modeling of Pb(II) coordination via classical molecular dynamics simulations was investigated to assess the possible use of non-bonded potentials for the description of the metal–ligand interaction. In particular, this study aimed at testing the capability of cationic dummy atom schemes—in which part of the mass and charge of the Pb(II) is fractioned in three or four sites anchored to the metal center—in reproducing the correct coordination geometry and, also, in describing the hard/soft borderline character of this cation. Preliminary DFT calculations were used to design two topological schemes, PB3 and PB4, that were subsequently implemented in the Amber force field and employed in molecular dynamics simulation of either pure water or thiol/thiolate-containing aqueous solutions. The PB3 scheme was then tested to model the binding of Pb(II) to the lead-sensing protein pbrR. The potential use of CDA topological schemes in the modeling of Pb(II) coordination was here critically discussed.
Highlights
The coordinative bond uncommonly combines high strength with reversibility, probably because of its dual, electrostatic and covalent nature
By testing the PB1, PB3, and PB4 schemes in the modeling of the Pb(II)-water system, we found that a higher consistency with both density functional theory (DFT) results and available experimental data is achieved by the use of cationic dummy atom (CDA) topologies
We assessed the use of cationic dummy atom (CDA) topological schemes for the classical molecular dynamics (MD) simulation of either hydration or protein coordination of the Pb(II) ion
Summary
The coordinative bond uncommonly combines high strength with reversibility, probably because of its dual, electrostatic and covalent nature. The HSAB theory introduced a paradigm that allows to assess the stability of a coordinative bond based on the metal and ligand properties, mostly reflecting their propensity to form mostly electrostatic (hard) or mostly covalent (soft) coordination [1,2,3,4]. A metal ion may manifest either hard or soft behavior depending on the ligands available in a certain molecular system. The biological media are fair examples of molecular systems containing both hard and soft ligands. Protein and/or other biomacromolecules may contain hydrophobic pockets confined out of the water bulk, where soft ligand groups may be present and generate
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