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.
The active site of the [Fen class="Chemical">Fe] 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.
Authors: Camilla Lambertz; Nils Leidel; Kajsa G V Havelius; Jens Noth; Petko Chernev; Martin Winkler; Thomas Happe; Michael Haumann Journal: J Biol Chem Date: 2011-09-19 Impact factor: 5.157
Authors: Markus Sitzmann; Iwona E Weidlich; Igor V Filippov; Chenzhong Liao; Megan L Peach; Wolf-Dietrich Ihlenfeldt; Rajeshri G Karki; Yulia V Borodina; Raul E Cachau; Marc C Nicklaus Journal: J Chem Inf Model Date: 2012-02-21 Impact factor: 4.956
Authors: Konstantinos D Vogiatzis; Mikhail V Polynski; Justin K Kirkland; Jacob Townsend; Ali Hashemi; Chong Liu; Evgeny A Pidko Journal: Chem Rev Date: 2018-10-30 Impact factor: 60.622
Authors: Mary Grace I Galinato; C Matthew Whaley; Dean Roberts; Peng Wang; Nicolai Lehnert Journal: Eur J Inorg Chem Date: 2011-03 Impact factor: 2.524