Time-dependent density functional theory study of cobalt corrinoids: Electronically excited states of coenzyme B12
Bibliographic record
Abstract
The analysis of the electronic spectra of adenosylcobalamin (AdoCbl) and its derivative in which the trans axial base was replaced by a water molecule (AdoCbi–H2O) has been performed by means of time-dependent density functional theory (TDDFT). The latter corresponds to the situation encountered in strongly acidic conditions. The TDDFT electronic transitions and oscillator strengths were calculated at the optimized B3LYP and BP86 ground state equilibrium geometries. A comparison of the orbital energy diagrams obtained with the B3LYP and BP86 functionals reveals a different orbital order and composition of the highest occupied and lowest unoccupied molecular orbitals. In B3LYP the lowest-energy transitions are of π∕d→π*, π∕d→σ*, and π∕d→d characters while in the case of BP86 they are mainly d∕π→π* and d→π*. The long range charge transfer transitions involving excitations from adenine π orbitals to antibonding corrin π* orbital can be observed at low energies, especially in BP86 results. Calculated electronic excitations were used to simulate the absorption spectra for a direct comparison with the absorption spectra recorded for AdoCbl at different pH values. As previously found for methylcobalamin [see Andruniów et al., J. Chem. Phys. 129, 085101 (2008)] also for AdoCbl the two-parameter scaling technique is required to obtain a satisfactory agreement between theoretical and experimental spectra. Both functionals correctly predict the shifting of the lowest intense transition toward blue by approximately 13nm upon changing pH from 7 to 1.
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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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.004 | 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".