DFT Study on the Conformational and Vibrational Properties of 3’-Deoxycytidine and Its Analogues
Bibliographic record
Abstract
Impact of saturation of the sugar C(3’)=C(4’) bond of acytidine nucleoside derivative, 3’, 4’-didehydro-3’-deoxycytidine (I) is revealed usingsimulated vibrational spectra, with respect to 3’-deoxycytidine. The density functional theory based calculations found that the C(3’)=C(4’) double bondrestricts the sugar flexibility and affects the sugar-base intramolecular hydrogen bond network. For 3’-dC, two minimal energy conformers are identified on the potential energy surface. The first conformer (IIA) takes anO4’-endo and gauche-gauche (gg) orientation whereas the second (IIB) has a C3’-exo and gauche-trans (gt) orientation in gas phase. The two conformers which have been observed previously in the crystal structure are separated by a low energy barrier. The carbon double bond in the sugar moiety of I confines the pseudorotation of the pentagon ring to be significantly flatter than that of the sugar ring in IIA and IIB. The simulated vibrational spectra, both in gas phase and in solutions, report such structural caused spectral changes with red and blue vibrational frequency shifts.The firsthydration shell of 3’-dC has been also investigated applying hybrid QM/MM molecular dynamic simulation.
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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) | 0.001 | 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) | 0.004 | 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".