RNA Structural Forms Studied by Vibrational Circular Dichroism: Ab Initio Interpretation of the Spectra
Bibliographic record
Abstract
Infrared (IR) and vibrational circular dichroism (VCD) spectra of single-stranded poly(rA) and poly(rU) RNA polynucleotides and double- and triple-stranded RNA helices were recorded and interpreted on the basis of density functional theory (DFT) at the BPW91/6-31G** level. Ab initio computations were performed for smaller fragments and extended to longer oligomers via transfer of atomic property tensors. The normal mode partial optimization method developed lately was found convenient for relaxation of the fragment geometries. Most of observed spectral features could be assigned to vibrations of the adenine, uracil, and sugar−phosphate chromophores; in particular, the VCD band shapes could be explained on the basis of specific spatial interactions. Thus, the VCD technique proved to be sensitive to various RNA conformational types (random coil, single strand, duplex, and triplex) in solution, spectra of which could be reliably modeled. The effect of the solvent could be only partially included, and ambiguity remains in the model structure used for the triplex RNA form.
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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 | 0.000 |
| 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) | 0.001 | 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".