Feasibility study of hydrogen-bonded nucleic acid base pairs in gas and water phases — A theoretical study
Bibliographic record
Abstract
To investigate the base pair binding probabilities for nucleic acid bases, numerous models were studied for contacts between adenine, thymine, guanine, cytosine, and uracil using density functional theory (DFT) in combination with the 6–311G* basis set. We obtained an assessment for the energy given by our calculations in gas and aqueous phases, which showed that it should be incorporated into hydrogen bonding and propeller rotational energies. The 42 complexes of base pairs (5 regular and 37 irregular base pairs) were proposed and their hydrogen-bonding (H-bonding) properties were verified. The hydrogen bonds in some irregular base pairs, including CC, UU, and TT (series 1), were stronger than in regular GC and AT base pairs. Also, the strength of the hydrogen bonds in the proposed base pairs, including CU, GG, GU, and TU (series 2), were similar to regular base pairs from an energetic point of view. The propeller rotations revealed a higher rotational barrier energy (6–7.5 kcal/mol; 1 cal = 4.184 J) for irregular base pairs (series 1 and 2) than regular GC and AT ones (1–3 kcal/mol). Nevertheless, the trend in these affinities of the complex contact probabilities and their biological properties were confirmed by our calculations.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.000 | 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".