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Berkeley Lab Earth Scientists Jill Banfield and Harry Beller explain the Sustainable Systems SFA 2.0 project's research on metabolic potential—or how metabolic lifestyles of microbial communities modulate in response to as well as influence environmental change.
Berkeley Lab Earth Scientist Ken Williams explains the watershed research within the Sustainable Systems SFA 2.0 project—including identification and monitoring of primary factors that control watershed biogeochemical functioning.
Berkeley Lab Earth Sciences Division Director Susan Hubbard, the Project Lead for the Sustainable Systems Scientific Focus Area (SFA) 2.0, gives an overview of the project and its mission to develop a predictive understanding of terrestrial environments, from the genome to the watershed scales, to enable a new class of solutions for environmental and energy solutions.
In redox processes in complex transition metal-containing species are often intimately associated with changes in ligand protonation states and metal coordination number. Moreover, 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 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 Co ligand binding equilibrium constants (Kon/off), pKas and reduction potentials for models of aquacobalamin in aqueous solution. We consider two models for cobalamin ligand coordination: the first follows the hexa, penta, tetra coordination scheme for Co III , Co II , and Co I species, respectively, and the second model features saturation of each vacant axial coordination site on Co II and Co I 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, we find that the accuracy of the computed properties is largely independent of the scheme used, but including only a continuum representation of the solvent 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 pK a s and 2.3 log units for two log K on/off values for the aquacobalamin system. Furthermore, we find that the BP86 functional commonly used in corrinoid studies suffers from erratic behavior and inaccurate descriptions of Co axial ligand binding, leading to substantial errors in predicted pK a s and K on/off values. Finally, these findings demonstrate the effectiveness of the present approach for computing electrochemical and thermodynamic properties of a complex transition metal-containing cofactor.