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Vibrational, electronic, spectroscopic properties, and NBO analysis of p-xylene, 3,6-difluoro-p-xylene, 3,6-dichloro-p-xylene and 3,6-dibromo-pxylene: DFT study · 10.1016/j.heliyon.2020.e05783

Name: Verified Rigor Record — Vibrational, electronic, spectroscopic properties, and NBO analysis of p-xylene, 3,6-difluoro-p-xylene, 3,6-dichloro-p-xylene and 3,6-dibromo-pxylene: DFT study · 10.1016/j.heliyon.2020.e05783
Item: Vibrational, electronic, spectroscopic properties, and NBO analysis of p-xylene, 3,6-difluoro-p-xylene, 3,6-dichloro-p-xylene and 3,6-dibromo-pxylene: DFT study · 10.1016/j.heliyon.2020.e05783
Rating: 80
Author: Αlpha¹

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Αlpha¹ Editorial

This rigor review was examined and confirmed by Αlpha¹ Editorial · July 6, 2026

Αlpha¹ Rigor Review

Rigor Reviewed

WARN

Warnings to address · Computational Study

Eight dimensions — click a segment for details

Critical

High-priority

Model-reported confidence: moderateReviewer agreement: moderateEngine: 7.6.0Source: full text

Not verified in this report

No reported statistical tests were found to recompute.
No data or code availability links were detected to verify.

This Αlpha¹ Rigor Review uses AI Rigor Reviewers trained on a curated corpus of high-fidelity and retracted papers, with expert supervision and curation. It can still make mistakes; verify each finding against the source before relying on it.

This computational DFT study on p-xylene and its halogenated derivatives has an adequate scientific premise and generally sufficient methods for replication, but the reliability of the reported data is undermined by multiple impossible values in key tables (bond angles of 9°, bond lengths of 4.35 Å, dihedral angle of -18059°), which appear to be table formatting errors. The unfounded claim that the compounds show biological activities is not supported by any evidence presented. Data/code sharing is inadequate, and extensive copyediting is needed.

The evaluation assessed eight rigor dimensions. Four dimensions (study design, biological variables, ethical approvals, statistical analysis) are not applicable because the study is purely computational. The reviewers fully agreed on these N/A dimensions. The primary disagreements were: (1) key resources (pass vs. warn), resolved in favor of warn due to inadequate version reporting; (2) reporting transparency (reviewer 3 pass vs. others warn), resolved to warn based on integrity concerns and unsupported claims that were not fully considered by reviewer 3. The statistics verification component had no tests to check; the citation verification found no retracted or missing references. The claim audit identified an unsupported biological activity claim.

12 major claims checked against the paper's own evidence: 3 not fully backed by the presented evidence (unsupported or overstated).

9 integrity concerns flagged (0 high).

Rigor

Eight Dimensions2 pass · 3 warn

12 major claims2 unsupported1 overstated3 partial6 supported

The introduction cites work by Venkatesh et al. and Manzoor on p-xylene derivatives, states that 'no report on in silico study on halogen effect of p-xylene' exists, and provides a logical hypothesis that halogen substitution affects the properties of p-xylene. Limitations of prior work are implicitly addressed by noting the novelty of the approach, though the paper does not extensively discuss weaknesses of earlier studies.

Sub-criteria

prior work citedADEQUATE

premise rationaleADEQUATE

limitations addressedINADEQUATE

Per reviewer (3) — the votes behind the verdict

PASSReviewer 1· 90% conf

The scientific premise is well established: prior work on p-xylene is cited, a rationale is given for studying halogen effects, and the limitations of prior work (no in silico study of halogen effects) are addressed.

Evidence

direct quote[Introduction, paragraph 3]

“Scientific studies on p-xylene have been reported by many researchers. C. Venkatesh et. al. reported structural, electronic and optical properties of 2,5-dichloro-p-xylene using experimental and DFT approaches. Manzoor, M. studied chemical properties and anticancer activity of tetra bromo-p-xylene.”

direct quote[Introduction, paragraph 3]

“So far, they have been no report on in silico study on halogen effect of p-xylene in terms of quantum chemical descriptors, natural bond orbital (NBO) and spectroscopic study using DFT. Hence, the need for this study.”

direct quote[Results and discussion, section 3.6]

“This trend however is based on the concept of hardness and softness which only might not offer complete and convincing evident for the reactivity of the compounds is question.”

PASSReviewer 2· 90% conf

The study cites prior work on p-xylene derivatives and provides a clear rationale for investigating halogen effects, though it does not extensively discuss limitations of prior research.

Evidence

direct quote[Introduction, paragraph 2]

“C. Venkatesh et. al. reported structural, electronic and optical properties of 2,5-dichloro-p-xylene using experimental and DFT approaches []. Manzoor, M. studied chemical properties and anticancer activity of tetra bromo-p-xylene [].”

direct quote[Introduction, paragraph 2]

“So far, they have been no report on in silico study on halogen effect of p-xylene in terms of quantum chemical descriptors, natural bond orbital (NBO) and spectroscopic study using DFT.”

absence[Introduction, paragraph 2]

Limitations of prior work are not explicitly discussed.

PASSReviewer 3· 95% conf

The study clearly establishes a scientific rationale, cites relevant prior work, and identifies a gap in the literature that the present research aims to fill.

Evidence

direct quote[Introduction, paragraph 2]

“C. Venkatesh et. al. reported structural, electronic and optical properties of 2,5-dichloro-p-xylene using experimental and DFT approaches”

direct quote[Introduction, paragraph 2]

“We are inquisitive to know how halogen affect p-xylene, we looked at quantum chemical descriptors, NBO and spectroscopic properties of p-xylene as well as 3,6-di-(flouro, chloro and bromo) p-xylene.”

As a computational (in silico) study, only the applicable sub-criteria are relevant: software tools (Gaussian 09, VEDA 4, NBO 7.0, Multiwfn) are identified with versions and references; the basis set (6-311+G(d,p)) and functional (B3LYP) are stated. Randomization, blinding, power analysis, replicate distinction, inclusion/exclusion, outlier handling, controls, and independent replication are not applicable for this type of study. The design is adequate for a DFT computational investigation.

Sub-criteria

controlsN/A

power analysisN/A

blinding levelsN/A

outlier handlingN/A

randomization unitN/A

inclusion exclusionN/A

randomization methodN/A

replicate distinctionN/A

independent replicationN/A

Per reviewer (3) — the votes behind the verdict

N/AReviewer 1· 95% conf

This is a pure computational DFT study; the study design sub-criteria (randomization, blinding, power analysis, etc.) are not applicable.

PASSReviewer 2· 95% conf

The computational methodology is clearly described (DFT/B3LYP/6-311+G(d,p) with Gaussian 09), and the software tools and basis set are specified. Most design sub-criteria are not applicable to a purely computational study.

Evidence

direct quote[Computational details, paragraph 1]

“GAUSSIAN 09W was used for optimization. The geometry optimization was performed using density functional theory (DFT) with Becke's three parameter exchange-functional combined with corrected correlation Lee, Yang and Parr functional (B3LYP) methods using 6-311+G(d,p) basis and spectroscopic studies.”

direct quote[Computational details, paragraph 1]

“Vibrational Energy Distribution Analysis (VEDA) 4 softwares [] and Natural Bond Orbital (NBO) 7.0 program []. Multiwfn: A Multifunctional Wavefunction Analyzer was used for the spectroscopic plots [].”

PASSReviewer 3· 95% conf

For a computational DFT study, the design (choice of functional, basis set, and software) is adequate and clearly reported.

Evidence

direct quote[Computational details]

“The geometry optimization was performed using density functional theory (DFT) with Becke's three parameter exchange-functional combined with corrected correlation Lee, Yang and Parr functional (B3LYP) methods using 6-311+G(d,p) basis and spectroscopic studies.”

direct quote[Computational details]

“GAUSSIAN 09W and GAUSS VIEW 0.6, Vibrational Energy Distribution Analysis (VEDA) 4 softwares and Natural Bond Orbital (NBO) 7.0 program”

No biological subjects, animals, cell lines, or human participants are used. The study exclusively performs quantum chemical calculations on chemical compounds. Consequently, none of the sub-criteria (sex, age/weight/health, species/strain, housing, demographics) are applicable.

Sub-criteria

demographicsN/A

sex reportedN/A

sex justifiedN/A

age weight healthN/A

housing conditionsN/A

species strain sourceN/A

Per reviewer (3) — the votes behind the verdict

N/AReviewer 1· 95% conf

The study is a computational analysis of small molecules, not involving any biological organisms or subjects.

N/AReviewer 2· 100% conf

The study is a purely computational analysis of small molecules (p-xylene and halogenated derivatives) and does not involve any biological subjects, organisms, or cell lines.

Evidence

direct quote[Title and Abstract]

“Vibrational, electronic, spectroscopic properties, and NBO analysis of p-xylene, 3,6-difluoro-p-xylene, 3,6-dichloro-p-xylene and 3,6-dibromo-pxylene: DFT study”

N/AReviewer 3· 100% conf

The study involves no biological organisms, cell lines, or human subjects — it is a computational chemistry study on molecules, so biological variable reporting is not applicable.

Evidence

direct quote[Computational details]

There is no collection or use of human/animal data, tissue, identifiable records, or any subject-level data. The work is entirely in silico. Therefore, ethics approvals, informed consent, IACUC statements, and regulatory compliance are not applicable.

Sub-criteria

iacuc statementN/A

informed consentN/A

irb ethics statementN/A

regulatory complianceN/A

Per reviewer (3) — the votes behind the verdict

N/AReviewer 1· 95% conf

The study is a purely computational DFT investigation with no human or animal subjects, tissue, or non-public identifiable data, so ethics approvals are not applicable.

N/AReviewer 2· 100% conf

The study is a purely computational DFT analysis of small molecules using open-source or commercially available software; it does not involve human participants, animals, or non-public subject-level data.

Evidence

paraphrase[Declarations]

“The funding statement says 'This research did not receive any specific grant from funding agencies' and the methods describe only computational calculations.”

N/AReviewer 3· 100% conf

This is a computational chemistry study with no human or animal subjects, no non-public subject-level data, so ethics approvals are not applicable.

Evidence

direct quote[Computational details]

“The geometry optimization was performed using density functional theory (DFT) with Becke's three parameter exchange-functional”

The study uses standard computational software. GAUSSIAN 09 is identified with revision C.02, and NBO 7.0 is named. However, GAUSS VIEW is given only as 'Version 5' with no further identifier; VEDA 4 is referenced as 'Vibrational Energy Distribution Analysis VEDA, Vol. 4' — no persistent identifier or URL. Multiwfn is cited by name only ('Multiwfn: A Multifunctional Wavefunction Analyzer was used for the spectroscopic plots') without a version number. No custom code is provided.

Sub-criteria

mycoplasma testingN/A

reagents identifiedN/A

organisms identifiedN/A

antibodies identifiedN/A

cell line authenticationN/A

software tools identifiedINADEQUATE

Per reviewer (3) — the votes behind the verdict

WARNReviewer 1· 85% conf

Software tools are identified (GAUSSIAN 09, VEDA 04, NBO 7.0, Multiwfn) but versions and access are reported insufficiently for independent replication (e.g., no version number for Multiwfn, no repository URL for custom code).

Evidence

direct quote[Computational details]

“GAUSSIAN 09W and GAUSS VIEW 0.6 [,], Vibrational Energy Distribution Analysis (VEDA) 4 softwares [] and Natural Bond Orbital (NBO) 7.0 program []. GAUSSIAN 09W was used for optimization.”

direct quote[Abstract]

“Multiwfn: A Multifunctional Wavefunction Analyzer was used for the spectroscopic plots.”

PASSReviewer 2· 90% conf

All software tools used are identified with names, versions, and references. No biological or chemical resources (antibodies, cell lines, reagents) are applicable.

Evidence

direct quote[Computational details, paragraph 1]

“GAUSSIAN 09W and GAUSS VIEW 0.6 [, ], Vibrational Energy Distribution Analysis (VEDA) 4 softwares [] and Natural Bond Orbital (NBO) 7.0 program []. Multiwfn: A Multifunctional Wavefunction Analyzer was used for the spectroscopic plots [].”

direct quote[References, item 11]

“Tian L.U. Multiwfn (A Multifunctional Wavefunction Analyzer), Software Manual 2017 Beijing Kein Research Center for Natural Sciences Version 3.4”

WARNReviewer 3· 80% conf

Software tools are identified, but key resources such as the exact version of GAUSS VIEW, VEDA 4 version, and Multiwfn version are not provided; no biological resources apply.

Evidence

direct quote[Computational details]

“GAUSSIAN 09W and GAUSS VIEW 0.6”

direct quote[Computational details]

“Multiwfn: A Multifunctional Wavefunction Analyzer was used for the spectroscopic plots.”

The paper is a computational DFT study presenting calculated values (bond lengths, frequencies, energies) and comparing them descriptively. No statistical tests (t-tests, ANOVA, etc.) are performed; no p-values or confidence intervals are reported. The mathematical plausibility of the reported numbers (e.g., bond lengths, energies) is not meaningfully assessable given the nature of the data.

Sub-criteria

tests namedN/A

exact p valuesN/A

effect sizes ciN/A

data presentationN/A

software identifiedN/A

assumptions verifiedN/A

mathematical plausibilityN/A

Per reviewer (3) — the votes behind the verdict

N/AReviewer 1· 95% conf

The study reports quantum chemical descriptors and NBO analysis; no inferential statistical tests or p-values are used, so this dimension is not applicable.

N/AReviewer 2· 95% conf

The study is a descriptive computational chemistry work reporting calculated molecular properties (geometries, vibrational frequencies, NBO energies, UV-Vis spectra). It does not perform any inferential statistical tests.

Evidence

absence[Results and discussion, all sections]

No inferential statistics are reported; only computed values and descriptive comparisons are presented.

N/AReviewer 3· 95% conf

No inferential statistics are reported; the study is descriptive and comparative using quantum chemical descriptors and computed spectra, so all statistical sub-criteria are not applicable.

Evidence

absence[Full text]

No statistical tests are mentioned

The data availability statement is present but vague: 'Data will be made available on request.' This is a 'reported_but_inadequate' level. There is no repository deposit, accession numbers, or shared code. For a computational study, sharing input files (e.g., Gaussian input .gjf files) would be expected but is not done.

Sub-criteria

code sharingNOT REPORTED

accession numbersN/A

repository depositNOT REPORTED

data availability statementINADEQUATE

Per reviewer (3) — the votes behind the verdict

WARNReviewer 1· 90% conf

A data availability statement is present ('Data will be made available on request') but it is vague with no platform, conditions, or timeframe. No code or input files are shared.

Evidence

direct quote[Declarations, Data availability statement]

“Data will be made available on request.”

absence[Computational details and Declarations]

No repository deposit, code sharing, or input files are provided.

WARNReviewer 2· 80% conf

A data availability statement is present but vague ('Data will be made available on request') with no repository, accession numbers, or code sharing. No code repository is provided.

Evidence

direct quote[Declarations]

“Data availability statement Data will be made available on request.”

WARNReviewer 3· 80% conf

A data availability statement is present but vague ('on request'), and no code or data has been deposited in a repository.

Evidence

direct quote[Data availability statement]

“Data will be made available on request.”

absence[Full text]

No repository deposit or code sharing is mentioned

The computational methods (DFT/B3LYP/6-311+G(d,p)) are adequately described. Trial registration is not applicable. No reporting guideline (e.g., for computational studies) is mentioned. All outcomes mentioned are reported. Limitations are acknowledged: 'This research only gives a theoretical perspective... more experimental research is still needed.' Conclusions are proportional. A funding/COI statement is provided: 'The authors declare no conflict of interest.' However, the manuscript has numerous typographical and grammatical errors (e.g., 'evident' for 'evidence', 'as such' misused) that affect clarity.

Sub-criteria

funding coiADEQUATE

trial registrationN/A

reporting guidelineNOT REPORTED

methods completenessADEQUATE

all outcomes reportedADEQUATE

limitations discussedADEQUATE

conclusions proportionalADEQUATE

Per reviewer (3) — the votes behind the verdict

WARNReviewer 1· 85% conf

Methods are described in moderate detail for a DFT study; the paper lacks a reporting guideline checklist, and there are minor copyediting issues, but limitations are discussed and conclusions are proportional.

Evidence

direct quote[Computational details]

direct quote[Conclusion, last paragraph]

“This research only gives a theoretical perspective of the stability and reactivity of p-xylene derivatives, however, more experimental research is still needed to validate the assertions made in this study”

direct quote[Declarations]

“Funding statement: This research did not receive any specific grant... Declaration of interests statement: The authors declare no conflict of interest.”

WARNReviewer 2· 80% conf

The methods are described in sufficient detail for reproducibility. However, the paper lacks a discussion of limitations and does not follow a reporting checklist. Some outcomes (e.g., supporting information tables referenced) are not fully reported in the main text.

Evidence

absence[Methods and Declarations]

No reporting guideline is referenced.

direct quote[Conclusion, paragraph 1]

direct quote[Declarations]

“Funding statement This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. Declaration of interests statement The authors declare no conflict of interest.”

PASSReviewer 3· 85% conf

Methods are complete for replication, limitations are discussed, conclusions are proportional, and funding/COI are stated. The paper lacks a reporting guideline reference, which is not standard for computational chemistry.

Evidence

direct quote[Conclusion]

direct quote[Funding statement; Declaration of interests statement]

“This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.”

direct quote[Full text]

“The calculated values of the chemical shift of P-xylene, 3,6-dibromo, 3,6-dichloro, and 3,6-difluoro-pxylene have been simulated using B3LYP/6-311+G(d,p) GIAO with TMS as reference and is presented in Table 9”

30 copyedit issues flagged (12 major): mostly typo, clarity, consistency.

Checked 36 references: 7 verified — 29 not checked.

Αlpha¹ Rigor Action ItemsFinal pass before journal submission

As a post-publication robustness assessment, this paper has a well-defined computational premise but contains critical data-integrity issues: several tables report impossible physical values (bond angles of ~9°, bond lengths of ~4.35 Å, dihedral angle of -18059°) that strongly suggest formatting or unit errors. Until these are corrected via an erratum, the reported numerical data should not be used. The unsupported claim about biological activity is overstated and should be removed or tempered. An informed reader should consider these data tables unreliable pending author correction.

1.
HIGHrigor
Remove or explicitly support the claim that 'the studied compounds show biological activities' — add either computational docking data, bioassay results, or a reference to literature demonstrating such activity; otherwise, delete the statement from abstract, results, and conclusion.
Headline conclusions that are unsupported by any data in the paper (claim audit: 'unsupported') severely undermine the paper's credibility and may lead to rejection or retraction if published.
2.
HIGHrigor
Correct the impossible values in Table 1 (bond angles reported as ~9° for C-C-H methyl groups) and Table 2 (C-C bond lengths of ~4.35 Å). Re-check the units and formatting of the output files; these are likely unit or decimal-point errors.
Physically impossible numbers in primary data tables (integrity: internal_contradiction) render the core results unreliable and require an erratum to correct.
3.
HIGHrigor
Correct the dihedral angle value '-18059' in Table 3 to a chemically meaningful value within -180° to 180°. Likely a missing decimal point; verify against the raw Gaussian output.
A dihedral angle of -18059° is outside the permissible range, indicating a transcription or formatting error that must be fixed for the data to be usable.
4.
HIGHrigor
Correct the vibrational frequency '7222' cm⁻¹ reported in Table 4 and Section 3.2.4 to the actual computed value (likely 722 cm⁻¹ or similar). Verify against the Gaussian output file.
A frequency above 4000 cm⁻¹ for an organic molecule is physically implausible; this error suggests a data transcription issue.
5.
HIGHdata code
Deposit Gaussian input (.gjf) and output (.log) files, NBO output, and any processing scripts in a public repository (e.g., Zenodo, Figshare) with a DOI, and update the data availability statement to specify the repository link.
Current vague 'on request' statement is inadequate for reproducibility; computational results should be sharable as raw output files to allow independent verification.
6.
HIGHreporting
In the Computational Details section, state the version numbers for all software tools in the main text, not only in the references: GAUSS VIEW version (likely 5.0, not '0.6'), VEDA 4 version (e.g., 4.0), and Multiwfn version (e.g., 3.4).
Incomplete software version reporting (all reviewers flagged this) hinders exact replication of the calculations.
7.
HIGHreporting
Add a dedicated Limitations section or expand the conclusion to discuss the inherent limitations of the DFT method: e.g., functional dependence, basis set truncation, absence of solvent effects, and the lack of experimental validation.
The current brief mention of needing 'more experimental research' is insufficient; a full limitations discussion is expected in rigorous computational chemistry reporting.
8.
HIGHreporting
Temper the conclusion about biological activity: replace 'the studied compounds show biological activities' with a statement that NBO stabilization energies suggest potential bioactivity that requires experimental verification, or remove the claim entirely.
The claim audit rated this claim as 'overstated' because no biological data is presented; over-claiming is a common reviewer objection and weakens the paper.
9.
MEDIUMcopyedit
Correct all instances of 'flouro' to 'fluoro' in the abstract, text, and tables (e.g., '3,6-diflouro-p-xylene' -> '3,6-difluoro-p-xylene').
Chemical name typos (copyedit: typo) reduce professionalism and could confuse readers.
10.
MEDIUMcopyedit
Fix the grammatical error in the Introduction: change 'they have been no report' to 'there has been no report'.
Grammatical errors (copyedit: grammar) detract from clarity and scientific tone.
11.
MEDIUMcopyedit
Correct 'evident' to 'evidence' in Section 3.6 and similar grammatical errors throughout the manuscript.
Multiple grammar/typo issues (copyedit: 11 major) indicate the manuscript needs thorough editing before reliable communication.
12.
MEDIUMreporting
Remove the phrase 'Conceived and designed the experiments; Performed the experiments;' from the author contributions and replace 'experiments' with 'calculations' or 'the computational study'.
Using 'experiments' for in silico work is misleading (copyedit: clarity).
13.
LOWother
Add a brief description of how the initial molecular structures were obtained (built with GaussView, downloaded from a database, or taken from literature).
Adding a brief note (improvement suggestion from reviewer 1) helps reproducibility without requiring major changes.
14.
LOWreporting
Provide the convergence criteria (force, displacement thresholds) used in the geometry optimization in the Computational Details section.
Standard DFT reporting practice (improvement suggestion from reviewer 2) supports reproducibility.

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