By combining density functional theory with continuum solvation, researchers developed a consistent computational approach for computing pH-dependent redox and ligand dissociation properties of a complex corrinoid cofactor. Specifically, the approach provides balanced accuracy for three thermochemical properties, yielding RMS errors of 80 mV for seven reduction potentials, 2.0 log units for five pKas, and 2.3 log units for two log Kon/off values for the aquacobalamin system.
These findings provide insight into the mechanism of Hg methylation by HgcA, which uses a corrinoid cofactor. The approach is more broadly applicable to modeling and simulation of other subsurface redox processes, which are known to play important roles in mercury speciation and transformation.
Redox processes in complex transition metal-containing species are often intimately associated with changes in ligand protonation states and metal coordination number. A major challenge is therefore to develop consistent computational approaches for computing pH-dependent redox and ligand dissociation properties of organometallic species. Reduction of the cobalt (Co) center in the vitamin B12 derivative aquacobalamin can be accompanied by ligand dissociation, protonation, or both, making these properties difficult to compute accurately. We examine this challenge here by using density functional theory and continuum solvation to compute cobalt–ligand binding equilibrium constants (Kon/off), pKas and reduction potentials for models of aquacobalamin in aqueous solution. Two models for cobalamin ligand coordination were considered: the first follows the hexa, penta, tetra coordination scheme for CoIII, CoII, and CoI species, respectively. The second model features saturation of each vacant axial coordination site on CoII and CoI species with a single, explicit water molecule to maintain six directly interacting ligands or water molecules in each oxidation state. Comparing these two coordination schemes in combination with five dispersion-corrected density functionals, findings showed that the accuracy of the computed properties is largely independent of the scheme used, and that varying the Co coordination number yields marginally better results than saturating the first solvation shell around Co throughout. PBE performs best, displaying balanced accuracy and superior performance overall, with RMS errors of 80 mV for seven reduction potentials, 2.0 log units for five pKas, and 2.3 log units for two log Kon/off values for the aquacobalamin system. Furthermore, the BP86 functional commonly used in corrinoid studies suffered from erratic behavior and inaccurate descriptions of Co–axial ligand binding, leading to substantial errors in predicted pKas and Kon/off values. These findings demonstrate the effectiveness of this approach for computing electrochemical and thermodynamic properties of a complex transition metal-containing cofactor.
Johnston, R.C., J. Zhou, J.C. Smith, and J.M. Parks. 2016. “Toward Quantitatively Accurate Calculation of the Redox-associated Acid-Base and Ligand Binding Equilibria of Aquacobalamin.” Journal of Physical Chemistry B. DOI: 10.1021/acs.jpcb.6b02701
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