Electronegativity-Driven Structured Environments in DNA and RNA: Vibronic Coupling, Quantum Overlays, and Nucleic Acid Dynamics—A Perspective

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

This manuscript is quite confusing as there does not seem to be much of a purpose to it and it is not written in a scientific fashion where claims have references attributed to them. an example is "Processive enzymes, polymerases, helicases, ribosomes, and repair complexes, tend to remain closely associated with the phosphate groups as they move along the strand." There are no references supplied.

I suspect this manuscript is written by AI and should not be accepted.

Author Response

I appreciate Reviewer 1’s comments and have addressed the substantive concerns raised. Several statements that previously lacked citations now include appropriate references, and I have clarified the purpose, scope, and scientific framing of the manuscript to improve readability and coherence.

Regarding the reviewer’s concern about authorship, I would like to clarify that the manuscript was written entirely by me. I have revised the text for clarity and strengthened the scientific grounding to ensure that the presentation reflects the standards expected for a scholarly Perspective.

Reviewer 2 Report

Comments and Suggestions for Authors

The manuscript proposes a framework, using electromagnetic architecture derived from Pauling EN patterns to describe nucleus acids. The topic is interesting and timely. However, several major issues need to be addressed before the paper can be reconsidered for publication. Overall, this paper is ambitious to establish a framework, yet without substantial grounding. I suggest the author proofread the manuscript one line after another to make sure every line is rigorously verified by physics laws or in current literature.

Major:

#1. Electronegativity on which the manuscript relies is an empirical atomic-scale concept, not a spatial field descriptor. Its direct extrapolation to define a structured “positional rail” is conceptually overstated and lacks quantitative justification.

#2. I do not think the claim that electronegativity patterns may induce meaningful “quantum overlays” in nucleic acids is supported by current evidence.

#3. The authors would need to substantially reformulate the theoretical framework in physically rigorous terms. This paper is speculative and descriptive without sufficient quantitative description.

Minor:

Pay attention to the following terms which I do not find they have been rigorously defined in physics: electromagnetic blueprint, positional rail system, quantum overlay, and anisotropic amplification.

This manuscript is under consideration as a “perspective”, so it merits a chance to revise.

Author Response

Please see the attached file.

Author Response File: Author Response.pdf

Reviewer 3 Report

Comments and Suggestions for Authors

The author presented a review on quantum overlaps and the prospects of structured media in DNA and RNA controlled by electronegativity of nucleic acid dynamics. The review may be interesting, however, it has a number of issues that need to be addressed, after which it can be reviewed again. Comments on improving the review:
1. The review considers only one method and does not compare it with other models of structured media in DNA and RNA.
2. For the review, the author has reviewed too few studies devoted to this topic. 
3. It is not entirely clear from the text whether the proposed model takes into account the different number of connections between different bases.
4. The section devoted to the proposed method should be expanded to include a rigorous mathematical formulation, notation, and necessary proofs/conclusions..  
5. It is necessary to improve the quality of the drawings, as some of the information on them is unreadable.
6. In the text, the author mentions the use of bioinformatics, it is necessary to expand the possible application of the theory, as well as consider possible applications in DNA cryptography.

Author Response

I thank Reviewer 3 for their constructive and forward‑looking suggestions, which have helped broaden the manuscript’s scholarly grounding and relevance.

Comment 1: The manuscript should engage more deeply with existing literature and alternative models.

Response: I have expanded the literature context substantially. Section 3 now explicitly compares the proposed framework to polaron‑based charge transport models, excitonic coupling frameworks, hydration‑shell and counterion‑condensation models, and non‑Markovian bath formulations used in open‑quantum‑systems treatments. Relevant citations have been added throughout.

Comment 2: The paper should expand its discussion of potential applications.

Response: Section 5 has been significantly expanded. In addition to experimental approaches (DFT, 2D IR spectroscopy, single‑molecule methods), I now discuss potential applications in computational biology, machine‑learning‑based nucleic acid modeling, and speculative applications in DNA/RNA cryptography. These additions address the reviewer’s request to explore broader implications.

Comment 3: The model should clarify how it accounts for differing numbers of atomic connections between bases.

Response: This point is now addressed explicitly in Section 3. I clarify that the framework inherently incorporates differences in heteroatom composition, hydrogen‑bonding capacity, intrinsic dipole moments, and ring‑current effects between bases, which generate base‑specific perturbation profiles superimposed on the invariant phosphate backbone.

Summary of Additional Revisions

In addition to the specific changes above, I have made several global improvements:

• softened language around the “positional rail” concept
• improved clarity and flow in Sections 2, 3, and 4
• revised the Abstract to align with the more measured tone
• improved the clarity and professionalism of figure captions
• expanded literature context and added missing citations

I believe these revisions have substantially strengthened the manuscript while preserving its conceptual and hypothesis‑generating character. I appreciate the opportunity to revise the work and remain available for any further changes the editor or reviewers may request.

Round 2

Reviewer 2 Report

Comments and Suggestions for Authors

I think this paper shares some ideas and proposes interesting theories for readers to learn and discuss. After addressing most of my concerns and acknowledging limitations, this paper is worth publication in Quantum Rep. However, I do have my reservation about using Pauling EN like a spatial descriptor of local electrostatics. 

The final thing: before publication, I hope the author can proofread this manuscript. I can see clearly some of the formatting issues.

1) 4.6 The “Magic Methyl’ Effect

2) For all the symbols, please use italicized fronts both in equations and text.

Author Response

I thank Reviewer 2 for their supportive evaluation and for noting that the manuscript is now suitable for publication after addressing the earlier concerns. I have incorporated the remaining requested revisions as follows:

Clarification regarding the use of Pauling electronegativity

To address the reviewer’s reservation about treating Pauling electronegativity as a spatial descriptor, I have added a clarifying sentence in Section 4.4 immediately following the vibronic‑coupling relation:

“Pauling electronegativity is used here only as a qualitative, atom‑resolved heuristic to highlight patterns in electron‑withdrawing tendency, not as a literal spatial electrostatic field.”

Formatting corrections

• The section title 4.6. The Magic Methyl Effect has been corrected and standardized.
• All mathematical symbols in the manuscript (including Hsystem, Hbath, Hint, and ∇E) have been italicized for consistency with standard formatting.
• Minor formatting inconsistencies (including subheading style and figure caption alignment) have been corrected throughout the manuscript.

I believe these revisions fully resolve the reviewer’s remaining comments.

Reviewer 3 Report

Comments and Suggestions for Authors

I thank the authors for their attentive attention to the reviewers' comments and the comments they made.

Author Response

I thank Reviewer 3 for their positive evaluation and for acknowledging the careful attention given to the previous round of comments. No further issues were raised.

I hope that the revised manuscript and this response satisfactorily address all remaining concerns. Thank you again for your consideration, and I look forward to the next steps in the review process.