New insight into the substituent effects on the hydrolytic deamination of saturated and unsaturated cytosine
Bibliographic record
Abstract
Abstract Ab initio calculations were carried out to understand the effect of electron donating groups (EDG) and electron withdrawing groups (EWG) at the C5 position of cytosine (Cyt) and saturated cytosine (H 2 Cyt) of the deamination reaction. Geometries of the reactants, transition states, intermediates, and products were fully optimized at the B3LYP/6‐31G(d,p) level in the gas phase as this level of theory has been found to agree very well with G3 theories. Activation energies, enthalpies, and Gibbs energies of activation along with the thermodynamic properties (Δ E , Δ H , and Δ G ) of each reaction were calculated. A plot of the Gibbs energies of activation (Δ G ‡ ) for C5 substituted Cyt and H 2 Cyt against the Hammett σ ‐constants reveal a good linear relationship. In general, both EDG and EWG substituents at the C5 position in Cyt results in higher Δ G ‡ and lower σ values compared to those of H 2 Cyt deamination reactions. C5 alkyl substituents (H, CH 3 , CH 2 CH 3 , CH 2 CH 2 CH 3 ) increase Δ G ‡ values for Cyt, while the same substituents decrease Δ G ‡ values for H 2 Cyt which is likely due to steric effects. However, the Hammett σ ‐constants were found to decrease at the C5 position of cytosine (Cyt) and saturated cytosine (H2Cyt) on the deamination reaction. Both Δ G ‡ and σ values decrease for the substituents Cl and Br in the Cyt reaction, while Δ G ‡ values increase and σ decrease in the H 2 Cyt reaction. This may be due to high polarizability of bromine which results in a greater stabilization of the transition state in the case of bromine compared to chlorine. Regardless of the substituent at C5, the positive charge on C4 is greater in the TS compared to the reactant complex for both the Cyt and H 2 Cyt. Moreover, as the charges on C4 in the TS increase compared to reactant, Δ G ‡ also increase for the C5 alkyl substituents (H, CH 3 , CH 2 CH 3 , CH 2 CH 2 CH 3 ) in Cyt, while Δ G ‡ decrease in H 2 Cyt. In addition, analysis of the frontier MO energies for the transition state structures shows that there is a correlation between the energy of the HOMO–LUMO gap and activation energies.
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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 | 0.000 | 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 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 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".