Quantum refinement of [FeFe] hydrogenase indicates a dithiomethylamine ligand.
The active site of the [FeFe] hydrogenases contains two Fe ions bound to one Cys ligand, three CO molecules, two CN(-) ions, and a dithiolate ligand. The nature of the last of these has been much discussed, and it has been suggested that it contains C, N, or O as the bridgehead atom. Most experimental studies indicate a N atom, whereas a recent density functional theory (DFT) study of a crystal structure indicated an O atom. Here, we performed quantum refinement on the same crystal structure with five different models of the dithiolate ligand X(CH(2)S(-))(2), with X = CH(2), NH(2)(+), NH (two conformations), or O; we found that structures with a N bridgehead atom actually provide the best fit to the raw crystallographic data. Quantum refinement is standard crystallographic refinement in which the molecular mechanics force field normally used to supplement the experimental raw data to give a more chemical structure is replaced by more accurate DFT calculations for the active site. Thereby, we obtain structures that are an ideal compromise between DFT and crystallography.
Ryde
Ulf
U
Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden. Ulf.Ryde@teokem.lu.se
Greco
Claudio
C
De Gioia
Luca
L
D003198:Computer Simulation; D006864:Hydrogenase / Q000737:chemistry* / Q000378:metabolism*; D007506:Iron-Sulfur Proteins / Q000737:chemistry* / Q000378:metabolism*; D008024:Ligands; D008744:Methylamines / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D011789:Quantum Theory; D014050:Toluene / Q000031:analogs & derivatives* / Q000737:chemistry
D007506:Iron-Sulfur Proteins; D008024:Ligands; D008744:Methylamines; D014050:Toluene; C027451:methylamine; C118830:iron hydrogenase; D006864:Hydrogenase; C004848:dithiol