Theoretical Investigation on the Origin of Yellow‐Green Firefly Bioluminescence by Time‐Dependent Density Functional Theory
Bibliographic record
Abstract
The question whether the emitter of yellow-green firefly bioluminescence is the enol or keto-constrained form of oxyluciferin (OxyLH(2)) still has no definitive answer from experiment or theory. In this study, Arg220, His247, adenosine monophosphate (AMP), Water324, Phe249, Gly343, and Ser349, which make the dominant contributions to color tuning of the fluorescence, are selected to simulate the luciferase (Luc) environment and thus elucidate the origin of firefly bioluminescence. Their respective and compositive effects on OxyLH(2) are considered and the electronic absorption and emission spectra are investigated with B3LYP, B3PW91, and PBE1KCIS methods. Comparing the respective effects in the gas and aqueous phases revealed that the emission transition is prohibited in the gas phase but allowed in the aqueous phase. For the compositive effects, the optimized geometry shows that OxyLH(2) exists in the keto(-1) form when Arg220, His247, AMP, Water324, Phe249, Gly343, and Ser349 are all included in the model. Furthermore, the emission maximum wavelength of keto(-1)+Arg+His+AMP+H(2)O+Phe+Gly+Ser is close to the experimental value (560 nm). We conclude that the keto(-1) form of OxyLH(2) is a possible emitter which can produce yellow-green bioluminescence because of the compositive effects of Arg220, His247, AMP, Water324, Phe249, Gly343, and Ser349 in the luciferase environment. Moreover, AMP may be involved in enolization of the keto(-1) form of OxyLH(2). Water324 is indispensable with respect to the environmental factors around luciferin (LH(2)).
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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) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| 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".