Modeling the Transition State Structures of the Reductive-Half Reaction Active Site of Xanthine Oxidase Bound to Guanine Analogues: A Density Functional Theory Approach
Bibliographic record
Abstract
Modeling and characterization the transition state structure of enzyme catalyzed reactions is essential. A DFT method employing B3LYP level of theory with 6-31G (d',p') basis set for non-metals and LanL2DZ basis set for molybdenum have been used. The bond orders of chemical fragments were calculated using AOmix softaware. The effect of chalcogen replacement, amine group and methyl group in the parent structure of xanthine bound to xanthine oxidase active site were compared. The transition state structure of model substrates (2AX, 2A6TP, 2A6SP and 2A6MP) bound to the truncated form of XO active site has been confirmed by the presence of one negative imaginary frequencies (s-1) (-60), (-140), (-230) and (-270), respectively. The corresponding normalized energy barriers (kcal/mol) from pre-transition state to the transition state, respectively, are (13.869), (21.753), (23.109) and (0.212). In this work, 2A6SP and 2A6TP substrates were found to be potential xanthine oxidase inhibitors. The large bond distances and minimum bond order for CRH-HRH bond, and small bond distances and maximum bond order for SMo-HRH bond at the transition state for chalcogen replaced 2AX confirms early transition state structure. Methyl substituted 2AX analog found to have post transition state structure. A potential xanthine oxidase inhibitor can be designed from purine family enzymes using DFT approach.
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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 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 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".