Using the density functional optimized active site geometries obtained in the accompanying paper (Lovell, T.; Li, J.; Noodleman, L. Inorg. Chem. 2001, 40, 5251), a combined density functional and electrostatics approach has been applied to further address attendant uncertainties in the protonation states of the bridging ligands for MMOH(ox). The acidities (pK(a)s) associated with the bridging H(2)O ligand in Methylococcus capsulatus and corresponding energetics of each active site cluster interacting with the protein environment have been evaluated. The pK(a) calculations in combination with the results of the gas phase DFT studies allow the active site cluster in Methylosinustrichosporium to be best described as a diiron unit bridged by 2OH(-) ligands having an overall neutral net cluster charge. The presence of the exogenous acetate in M. capsulatus reveals a diiron unit bridged by 1OH(-) and 1H2O which asymmetrically shares its proton with a second-shell acetate in a very short strong AcO..H...OH hydrogen bond. For all MMOH(ox) and MMOH(red) active sites examined, significant Fe-ligand covalency is evident from the ESP atom charges, consistent with very strong ligand --> metal charge transfer from the muOH(-) and mu-carboxylato bridging ligands. The magnitude of electrostatic interaction of the individual protein residues in the active domain with the active site has been assessed via an energy decomposition scheme. Important second-shell residues are highlighted for the next level of quantum mechanics based calculations or alternatively for site-directed mutagenesis studies. Finally, from the known structural and spectroscopic evidence and the DFT studies, a possible mechanism is suggested for the conversion of MMOH(ox) into MMOH(red) that involves a combination of protein residues and solvent-derived ligands from the second coordination sphere.