Spectroscopic, computational, and kinetic studies of the mu4-sulfide-bridged tetranuclear CuZ cluster in N2O reductase: pH effect on the edge ligand and its contribution to reactivity
Bibliographic record
Abstract
A combination of spectroscopy and DFT calculations has been used to evaluate the pH effect at the Cu Z site in Pseudomonas nautica (Pn) N 2 OR and Achromobacter cycloclastes (Ac) N 2 OR and its relevance to catalysis.Absorption, MCD, EPR with sulfur K-edge XAS spectra of the enzymes at high and low pH show minor changes.However, resonance Raman (rR) spectroscopy of PnN 2 OR at high pH shows that the 415 cm -1 Cu-S vibration (observed at low pH) shifts to higher frequency, loses intensity and obtains a 9 cm -1 18 O shift, implying significant Cu-O character, demonstrating the presence of a OH -ligand at the Cu I Cu IV edge.From DFT calculations both protonation of the OH -to H 2 O or the μ 4 -S 2-to μ 4 -SH -would produce large spectral changes which are not observed.Alternatively, DFT calculations including a lysine residue at an H-bonding distance from the Cu I Cu IV edge ligand show that the position of the OH -ligand depends on the protonation state of the lysine.This would change the coupling of the Cu-(OH) stretch with the Cu-S stretch, as observed in the rR spectrum.Thus the observed pH effect (pK a ~9.2) likely reflects protonation equilibrium of the lysine residue which would both raise E 0 and provide a proton for lowering the barrier for the N-O cleavage and for reduction of the [Cu 4 S(im) 7 OH] 2+ to the fully reduced 4Cu I active form for turnover.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 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 source (direct Gemma or distilled Codex), 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".