Ab Initio Study of the Deamination of Formamidine
Bibliographic record
Abstract
The mechanism for the deamination of formamidine with OH -, H 2 O, and H 3 O + was investigated using computational techniques. Optimized geometries for reactants, intermediates, products, and transition states were determined at the RHF/6-31G(d) and MP2/6-31G(d) levels of theory. Single-point energies were determined at G1 and G2 and using density functional theory (B3LYP) at both optimized geometries and the 6-311G(d,p), 6-311+G(d,p), 6-311++G(d,p) (with OH - only), 6-311G(2df,p), and 6-311+G(3df,2p) basis sets. Frequencies were calculated for all structures studied at both geometries. Intrinsic reaction coordinate analysis was carried out for all transition states. Activation energies were calculated for each pathway investigated. Deamination with H 3 O + involves the formation of the same tetrahedral intermediate from the addition of water to either possible protonated formamidine cation followed by a 1,3-proton shift and dissociation to products. Deamination is an unlikely event because of the high activation-energy barrier to the formation of the intermediate (242.4 kJ mol -1 for pathway A and 243.5 kJ mol -1 for pathway B using G2 data). Two pathways for deamination with H 2 O were studied. Pathway A produced a tetrahedral intermediate by the addition of water followed by a 1,3-proton shift and dissociation to products, and pathway B involved the formation of the tautomer of the formamide product by reaction with water followed by a 1,3-proton shift to yield formamide. Deamination by either pathway is unlikely because of the high activation-energy barriers involved (212.7 kJ mol -1 for the formation of the tetrahedral intermediate of pathway A and 249.2 kJ mol -1 for the formation of the formamide tautomer of pathway B using G2 data). Deamination with OH - yields a tetrahedral intermediate with a much lower activation-energy barrier than for the reaction with H 3 O + and H 2 O (58.2 kJ mol -1 using G2 data), but the deprotonation of formamidine by hydroxide appears to be the most likely process because of the resonance-stabilized deprotonated formamidine anion/water complex formed (Δ E = −163.2 kJ mol -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 | 0.001 |
| 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 | 0.001 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.004 | 0.001 |
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".