A new structural model for NiFe hydrogenases: an unsaturated analogue of a classic hydrogenase model leads to more enzyme-like Ni—Fe distance and interplanar fold
Bibliographic record
Abstract
The complex cation in the title compound, (carbonyl-1κ C )(1η 5 -pentamethylcyclopentadienyl)(μ-2,3,9,10-tetramethyl-1,4,8,11-tetrathiaundeca-2,9-diene-1,11-diido-1κ 2 S , S ′′′:2κ 4 S , S ′, S ′′, S ′′′)ironnickel( Fe — Ni ) hexafluorophosphate, [FeNi(C 10 H 15 )(C 11 H 18 S 4 )(CO)]PF 6 or [Ni( L ′)FeCp*(CO)]PF 6 , is composed of the nickel complex fragment [Ni( L ′)] coordinated as a metalloligand (using S 1 and S 4 ) to the [FeCp*(CO)] + fragment, where ( L ′) 2− is [S—C(Me)=C(Me)—S—(CH 2 ) 3 —S—C(Me)=C(Me)—S] 2− and where Cp* − is cyclo -C 5 (Me) 5 − (pentamethylcyclopentadienyl). The ratio of hexafluorophosphate anion per complex cation is 1:1. The structure at 150 K has orthorhombic ( Pbcn ) symmetry. The atoms of the complex cation are located on general positions (multiplicity = 8), whereas there are two independent hexafluorophosphate anions, each located on a twofold axis (Wyckoff position 4 c ; multiplicity = 4). The structure of the new dimetallic cation [Ni( L ′)FeCp*(CO)] + can be described as containing a three-legged piano-stool environment for iron [Cp*Fe(CO)`S 2 '] and an approximately square-planar `S 4 ' environment for Ni. The NiS 2 Fe diamond-shaped substructure is notably folded at the S—S hinge: the angle between the NiS 2 plane and the FeS 2 plane normals is 64.85 (6)°. Largely because of this fold, the nickel–iron distance is relatively short, at 2.9195 (8) Å. The structural data for the complex cation, which contains a new unsaturated `S 4 ' ligand (two C=C double bonds), provide an interesting comparison with the known NiFe hydrogenase models containing a saturated `S 4 '-ligand analogue having the same number of carbon atoms in the ligand backbone, namely with the structures of [Ni( L )FeCp(CO)] + (as the PF 6 − salt, CH 2 Cl 2 solvate) and [Ni( L )FeCp*(CO)] + (as the PF 6 − salt), where ( L ) 2− is [S—CH 2 —CH 2 —S—(CH 2 ) 3 —S—CH 2 —CH 2 —S] 2− and Cp − is cyclopentadienyl. The saturated analogues [Ni( L )FeCp(CO)] + and [Ni( L )FeCp*(CO)] + have similar Ni—Fe distances: 3.1727 (6), 3.1529 (7) Å (two independent molecules in the unit cell) and 3.111 (5) Å, respectively, for the two complexes, whereas [Ni( L ′)FeCp*(CO)] + described here stands out with a much shorter Ni—Fe distance [2.9196 (8) Å]. Also, [Ni( L )FeCp(CO)] + and [Ni( L )FeCp*(CO)] + show interplanar fold angles that are similar between the two: 39.56 (5), 41.99 (5) (independent molecules in the unit cell) and 47.22 (9) °, respectively, whereas [Ni( L ′)FeCp*(CO)] + possesses a much more pronounced fold [64.85 (6)°]. Given that larger fold angles and shorter Ni—Fe distances are considered to be structurally closer to the enzyme, unsaturation in an `S 4 '-ligand of the type (S—C 2 —S—C 3 —S—C 2 —S) 2− seems to increase structural resemblance to the enzyme for structural models of the type [Ni(`S 4 ')FeCp R (CO)] + (Cp R = Cp or Cp*).
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.000 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.000 | 0.001 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".