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Record W2886737079 · doi:10.1107/s2056989018010939

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

2018· article· en· W2886737079 on OpenAlexafffund
Daniel J. Harrison, Alan J. Lough, Ulrich Fekl

Bibliographic record

VenueActa Crystallographica Section E Crystallographic Communications · 2018
Typearticle
Languageen
FieldEnergy
TopicMetalloenzymes and iron-sulfur proteins
Canadian institutionsUniversity of Toronto
FundersNatural Sciences and Engineering Research Council of CanadaUniversity of Toronto
KeywordsChemistryHexafluorophosphateCrystallographyOrthorhombic crystal systemNickelStereochemistryCrystal structureHydrogenaseOctahedronEnzyme

Abstract

fetched live from OpenAlex

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*).

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

How this classification was reachedexpand

Full frame distilled prediction

Teacher imitation

Not 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.

metaresearch head score (Codex)0.001
metaresearch head score (Gemma)0.000
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesMeta-epidemiology (narrow)
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Simulation or modeling · Consensus signal: none
GenreCandidate signal: Empirical · Consensus signal: Empirical
Teacher disagreement score0.913
Threshold uncertainty score0.999

Codex and Gemma teacher scores by category

CategoryCodexGemma
Metaresearch0.0010.000
Meta-epidemiology (narrow)0.0010.001
Meta-epidemiology (broad)0.0010.001
Bibliometrics0.0020.003
Science and technology studies0.0010.001
Scholarly communication0.0000.001
Open science0.0020.001
Research integrity0.0010.001
Insufficient payload (model declined to judge)0.0000.000

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.

Opus teacher head0.029
GPT teacher head0.283
Teacher spread0.254 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it

Classification

machine, unvalidated

Machine predicted; a candidate call from one teacher head, not a consensus.

Study designSimulation or modeling
Domainnot available
GenreEmpirical

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".

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Citations3
Published2018
Admission routes2
Has abstractyes

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