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Investigations on 2-(4-Cyanophenylamino) acetic acid by FT-IR,FT-Raman, NMR and UV-Vis spectroscopy, DFT (NBO, HOMO-LUMO, MEP and Fukui function) and molecular docking studies · 10.1016/j.heliyon.2020.e04976

Name: Verified Rigor Record — Investigations on 2-(4-Cyanophenylamino) acetic acid by FT-IR,FT-Raman, NMR and UV-Vis spectroscopy, DFT (NBO, HOMO-LUMO, MEP and Fukui function) and molecular docking studies · 10.1016/j.heliyon.2020.e04976
Item: Investigations on 2-(4-Cyanophenylamino) acetic acid by FT-IR,FT-Raman, NMR and UV-Vis spectroscopy, DFT (NBO, HOMO-LUMO, MEP and Fukui function) and molecular docking studies · 10.1016/j.heliyon.2020.e04976
Rating: 58
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: highReviewer 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.

The paper has adequate methods reporting and a clear rationale, but it is critically lacking in data/code availability — a prerequisite for reproducibility in computational work — and the conclusion is overstated relative to the docking-only evidence. Minor reporting gaps (missing catalog number, no limitations section) further weaken transparency.

Three independent rigor evaluations were synthesized; all agreed on most dimensions except study design (one fail vs. two not applicable, resolved as not applicable). The copyedit pass flagged 25 issues (2 major, both the same internal contradiction in binding energy). Citation and statistics checks found no retracted references or re-computable tests, respectively; the insufficient coverage of these components is a caveat.

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

5 integrity concerns flagged (1 high).

Rigor

Eight Dimensions3 warn · 1 fail

12 major claims3 overstated2 partial7 supported

Prior work is cited (references 1-8 in introduction) and a rationale for studying the compound is given (hypercoagulable diseases). However, the strengths and weaknesses of prior research are not discussed, and no explicit limitations of prior work are addressed. The premise rationale is logical but the gaps in prior research are not identified.

Sub-criteria

prior work citedINADEQUATE

premise rationaleADEQUATE

limitations addressedNOT REPORTED

Per reviewer (3) — the votes behind the verdict

WARNReviewer 1· 70% conf

The paper cites prior work and establishes a rationale but does not address limitations of prior research.

Evidence

direct quote[Introduction, paragraph 1]

“Literaturesurvey, points out that a complete quantum mechanical calculation for the selected title compound has not yet been reported so far.”

paraphrase[Introduction]

“Paraphrase: The introduction states that hypercoagulable is dangerous and early identification is essential, motivating the study of 24CPA.”

absence[Introduction]

Limitations of prior research are not addressed.

WARNReviewer 2· 80% conf

The scientific premise is partially established: prior work is cited and a rationale is provided, but the paper does not critically discuss limitations of prior research or acknowledge weaknesses.

Evidence

paraphrase[Section 1. Introduction, paragraph 1]

“The introduction cites several references but does not discuss their strengths or weaknesses; it only states that a complete quantum mechanical calculation for this compound has not been reported.”

direct quote[Section 1. Introduction]

“Quantum chemical calculations, and molecular modeling are playing a major role for drug design and research vibrational spectroscopy.”

absence[Section 1. Introduction]

No explicit discussion of limitations of prior research

WARNReviewer 3· 75% conf

The paper cites prior work and provides a rationale for the study, but it does not clearly address limitations of prior research.

Evidence

direct quote[Introduction, paragraph 1]

“Literature survey, points out that a complete quantum mechanical calculation for the selected title compound has not yet been reported so far.”

direct quote[Introduction, paragraph 1]

“The 2-(4-Cyanophenylamino) acetic acid (24CPA) is used as a Hypercoagulable diseases.”

absence[Introduction]

No discussion of limitations in the prior work is found.

The study involves quantum chemical calculations and experimental spectroscopy for validation, without any interventional, observational, or comparative experimental design that would require the sub-criteria in this dimension. All sub-criteria are rated not_applicable as per study-type mapping for computational work.

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

FAILReviewer 1· 90% conf

The study is computational and lacks essential design elements such as outlier handling, controls, and independent replication.

Evidence

direct quote[Experimental method, paragraph 1]

“2-(4-Cyanophenylamino) acetic acid was purchased from Sigma-Aldrich company with 99% purity and used as such without further processing”

absence[Methods and Results]

No power analysis, outlier handling, controls, or independent replication reported.

N/AReviewer 2· 95% conf

The study is a single-molecule computational analysis with no experimental design features (randomization, blinding, power analysis, etc.) that the dimension assesses.

Evidence

paraphrase[Sections 2 and 3]

“The methods describe spectroscopy and DFT calculations; there is no randomization, blinding, power analysis, or comparative groups.”

N/AReviewer 3· 85% conf

This is a computational study with experimental spectroscopic validation; typical preclinical trial design elements are not applicable, and none are described.

Evidence

direct quote[Methods, section 3]

“The optimized structure of 24CPA was arrived from Gaussian 09 software by DFT-B3LYP method, 6–311++G(d,p) higher-order basis set.”

direct quote[Methods, section 2]

“2-(4-Cyanophenylamino) acetic acid was purchased from Sigma-Aldrich company with 99% purity and used as such without further processing.”

No human, animal, or cell-based subjects are used; the study focuses on a chemical compound and computational modeling.

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· 100% conf

The study is computational and uses a chemical compound; no biological variables are applicable.

N/AReviewer 2· 95% conf

The study does not involve biological subjects or specimens; it is a chemical compound analysis.

Evidence

paraphrase[Sections 2 and 3]

“The experiment involves a purchased chemical compound; no animals, humans, or cell lines are mentioned.”

N/AReviewer 3· 80% conf

This study is computational and uses a single synthesized chemical compound; no animal or human subjects are involved, so biological variables are not applicable.

Evidence

direct quote[Title and Methods]

“Investigations on 2-(4-Cyanophenylamino) acetic acid by FT-IR, FT-Raman, NMR and UV-Vis spectroscopy, DFT ... and molecular docking studies”

Ethics approval is not required for chemical analysis and computational modeling without biological samples.

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· 100% conf

No human or animal subjects are involved; the study uses a commercial chemical and computational methods.

N/AReviewer 2· 95% conf

The study does not involve human or animal subjects or non-public subject-level data; no ethics approval is required.

Evidence

paraphrase[Section 2. Experimental method]

“The compound was purchased from Sigma-Aldrich and used as such; no human or animal subjects mentioned.”

N/AReviewer 3· 85% conf

The study involves no human subjects, animals, or non-public identifiable data; ethics approvals are not applicable.

Evidence

direct quote[Methods, section 2]

“2-(4-Cyanophenylamino) acetic acid was purchased from Sigma-Aldrich company with 99% purity and used as such without further processing.”

The paper identifies the investigational compound as '2-(4-Cyanophenylamino) acetic acid' purchased from Sigma-Aldrich with 99% purity, but no catalog number or lot number is provided (inadequate). Software tools (Gaussian 09, VEDA4, Autodock 4.2.6, Swiss ADME) are named with versions, which is adequate. Other resource criteria (antibodies, cell lines, organisms) are not applicable.

Sub-criteria

mycoplasma testingN/A

reagents identifiedINADEQUATE

organisms identifiedN/A

antibodies identifiedN/A

cell line authenticationN/A

software tools identifiedADEQUATE

Per reviewer (3) — the votes behind the verdict

WARNReviewer 1· 70% conf

The compound and software are identified, but without catalog numbers or RRIDs, and custom code is not shared.

Evidence

direct quote[Experimental method, paragraph 1]

“2-(4-Cyanophenylamino) acetic acid was purchased from Sigma-Aldrich company with 99% purity”

direct quote[Computational methodology]

“Gaussian 09 software by DFT-B3LYP method, 6–311++G(d,p) higher-order basis set. The potential energy distribution and vibrational assignments were obtained using VEDA4 software”

absence[Methods]

No RRIDs or catalog numbers provided.

WARNReviewer 2· 80% conf

The chemical reagent is identified but lacks catalog number; software tools are adequately identified with versions. One of two applicable criteria is inadequate.

Evidence

direct quote[Section 2. Experimental method]

“2-(4-Cyanophenylamino) acetic acid was purchased from Sigma-Aldrich company with 99% purity”

direct quote[Section 3. Computational methodology]

“optimized structure of 24CPA was arrived from Gaussian 09 software by DFT-B3LYP method”

direct quote[Section 3. Computational methodology]

“Autodock 4.2.6 software”

WARNReviewer 3· 75% conf

The software tools are identified, but the chemical compound (the sole biological/chemical resource) is not identified with a catalog number or RRID; no antibodies, cell lines, or organisms are used.

Evidence

direct quote[Methods, section 2]

“2-(4-Cyanophenylamino) acetic acid was purchased from Sigma-Aldrich company with 99% purity”

direct quote[Methods, section 3]

“The optimized structure of 24CPA was arrived from Gaussian 09 software by DFT-B3LYP method, 6–311++G(d,p) higher-order basis set.”

Reported values include vibrational frequencies, energies, and docking scores without statistical comparisons or p-values. No statistical tests are performed.

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· 100% conf

The study does not use inferential statistics; it reports spectroscopic and computational results without hypothesis tests.

N/AReviewer 2· 95% conf

The study does not use inferential statistics; it reports computed energies, spectroscopic assignments, and docking results without hypothesis testing or p-values.

Evidence

paraphrase[Sections 4 and 5]

“The paper reports computational values and experimental spectra; no p-values, test statistics, or uncertainty measures are given.”

N/AReviewer 3· 80% conf

No inferential statistical tests are performed; the data are presented as comparisons of computational and experimental values without formal hypothesis testing.

Evidence

direct quote[Results and Discussion]

“The experimental bond length of O1–C12 is 1.328 Å and corresponding theoretical values are 1.346 Å.”

The paper lacks any data availability statement. Experimental spectra and computational output are not deposited in a repository. Custom code (THERMO.PL) is mentioned but not provided. This severely limits reproducibility.

Sub-criteria

code sharingNOT REPORTED

accession numbersNOT REPORTED

repository depositNOT REPORTED

data availability statementNOT REPORTED

Per reviewer (3) — the votes behind the verdict

FAILReviewer 1· 90% conf

No data availability statement is provided; experimental and computational data are not deposited; custom code is not shared.

Evidence

absence[Declarations section]

No data availability statement present.

absence[Entire manuscript]

No repository deposit or accession numbers.

direct quote[Computational methodology]

“Thermodynamics properties like entropy, enthalpy, and heat capacity values are obtained by THERMO. PL script [] with the Gaussian output file.”

FAILReviewer 2· 90% conf

No data availability statement, no repository deposit, no accession numbers, and no code sharing are provided.

Evidence

absence[Entire manuscript]

No data availability statement

absence[Entire manuscript]

No repository deposit or accession numbers

absence[Entire manuscript]

No code sharing mentioned

FAILReviewer 3· 90% conf

No data availability statement, repository deposit, accession numbers, or code sharing is provided; the paper fails all applicable criteria.

Evidence

absence[Entire paper]

No data availability statement is present.

Methods are detailed enough for replication (software, basis sets, and procedures described). All outcomes planned are reported. Funding and conflict of interest are transparently stated. However, the paper does not discuss limitations of the study, does not reference any reporting guideline (like ARRIVE/CONSORT, though not standard for this type), and the conclusion that the compound is a 'good anti hypercoagulable agent' overstates the docking-only evidence.

Sub-criteria

funding coiADEQUATE

trial registrationN/A

reporting guidelineNOT REPORTED

methods completenessADEQUATE

all outcomes reportedADEQUATE

limitations discussedNOT REPORTED

conclusions proportionalINADEQUATE

Per reviewer (3) — the votes behind the verdict

PASSReviewer 1· 60% conf

Methods are described, funding and conflicts are stated, but limitations are not discussed.

Evidence

paraphrase[Sections 2 and 3]

“Paraphrase: The experimental and computational methods sections provide sufficient detail on instrumentation, parameters, and software.”

absence[Conclusion]

No limitations section.

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. Competing interest statement The authors declare no conflict of interest.”

WARNReviewer 2· 85% conf

Methods are complete and funding/COI are disclosed, but limitations are not discussed, no reporting guideline is mentioned, and the main conclusion is somewhat overstated given the evidence.

Evidence

absence[Section 5. Conclusion]

No limitations discussed

direct quote[Abstract and Section 5. Conclusion]

“Molecular docking studies binding energy -5.45 kcal/mol confirm that this compound is a good anti hypercoagulable agent”

direct quote[Declarations]

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

WARNReviewer 3· 75% conf

Methods are described in reasonable detail, limitations are not discussed, and some claims are overstated relative to the evidence. No trial registration or reporting guideline is applicable.

Evidence

direct quote[Methods sections 2 and 3]

“By using PERKIN ELMER FTIR spectrometer the FT-IR spectrum recorded in the range 4000–450 cm −1 was taken in evacuation mode by KBr pellet method with resolution 1.0 cm −1.”

absence[Discussion/Conclusion]

No limitations are discussed.

direct quote[Conclusion]

“Molecular docking studies binding energy -5.45 kcal/mol confirm that this compound is a good anti hypercoagulable agent”

25 copyedit issues flagged (2 major): mostly typo, grammar, consistency.

Checked 48 references: 28 verified — 20 not checked.

Αlpha¹ Rigor Action ItemsFinal pass before journal submission

In this post-publication audit, the paper is of moderate robustness for its descriptive computational content but has significant reproducibility gaps: no data or code are available, and there is a clear internal contradiction in the reported binding energy that undermines the main conclusion. An informed reader should treat the key docking result with caution and consider the anti-hypercoagulable claim as unsupported speculation. The authors should consider issuing a correction to reconcile the binding energy values and to deposit supporting data and code.

1.
HIGHdata code
Add a Data Availability Statement specifying where raw spectral data (FT-IR, FT-Raman, NMR, UV-Vis) and computational output files (Gaussian .log, .chk) can be accessed, ideally via a repository like Zenodo or Figshare with a DOI.
The complete absence of a data availability statement and any deposited data severely limits reproducibility and is a red flag for readers and future users of the work.
2.
HIGHdata code
Deposit the custom THERMO.PL script in a public code repository (e.g., GitHub with a permanent identifier) and reference it in the manuscript.
The script is mentioned but not provided, making the thermodynamic calculations unreproducible.
3.
HIGHrigor
Reconcile the binding energy value for the 24CPA-4NV2 docking: the text (Abstract, Section 4.11, Conclusion) reports -5.45 kcal/mol but Table 10 shows -7.55 kcal/mol; correct both to the true value and ensure consistency throughout.
This internal contradiction is a factual error that undermines the core conclusion of the paper and would mislead readers.
4.
HIGHreporting
Rewrite the conclusion that 'this compound is a good anti hypercoagulable agent' to state that the docking result suggests a potential interaction requiring experimental validation, not a confirmed therapeutic effect.
A single docking score (even if consistent) cannot confirm biological activity; the current claim is overstated and unsupported.
5.
HIGHreporting
Add a formal Limitations section (e.g., within the Conclusion) discussing caveats such as gas-phase calculations, single protein target (4NV2), lack of experimental biological validation, and dependence on the chosen basis set/functional.
The omission of any limitations discussion leaves the reader unaware of the study's scope and potential biases.
6.
HIGHrigor
Provide the Sigma-Aldrich catalog number (and lot number, if available) for the compound 24CPA in the Experimental section.
A reagent identified by vendor and purity alone cannot be uniquely traced; a catalog number is essential for reproducibility.
7.
HIGHcopyedit
Correct the subject-verb agreement error in the Abstract: change 'Extensive quantum chemical calculation have been carried out' to 'Extensive quantum chemical calculations have been carried out'.
This is a basic grammar error that appears in the first sentence of the abstract and affects first impressions.
8.
HIGHcopyedit
Fix the missing space in 'Literaturesurvey' (Introduction, paragraph 1) to 'Literature survey' and remove the extraneous comma.
This typo in a key introductory sentence suggests poor editorial oversight.
9.
HIGHcopyedit
Correct the garbled sentence in Introduction, paragraph 1: 'The 2-(4-Cyanophenylamino) acetic acid (24CPA) is used as a Hypercoagulable diseases' to something like '24CPA is used to treat hypercoagulable diseases' or '24CPA is associated with hypercoagulable states'.
The current phrasing is grammatically incorrect and confusing.
10.
MEDIUMreporting
Specify the full version/revision number for all software tools, especially VEDA4 (version not stated) and Gaussian 09 (revision letter not given).
Incomplete version information reduces the precision of computational reproducibility.
11.
MEDIUMcopyedit
Ensure all range indicators use en-dashes (e.g., '3400–3500 cm⁻¹' instead of '3400-3500cm −1') and include proper spacing before units.
Formatting inconsistencies in units and ranges appear throughout the manuscript and are corrected during copyediting.
12.
MEDIUMcopyedit
Separate author names with commas in the author list (e.g., 'Rahuman, M.H.; Muthu, S.; Raajaraman, B.R.; Raja, M.; Umamahesvari, H.')
Author names are run together without separators, making attribution ambiguous.
13.
MEDIUMcopyedit
Replace placeholder empty brackets with proper citation numbers in the Introduction (e.g., '[ , , , , ]' with '[1,2,3,4,5]').
Empty brackets are an obvious formatting artifact that suggests incomplete editing.
14.
MEDIUMcopyedit
Define all abbreviations in Table 2 footnote (e.g., γs, γas, roc, w, sci, twi, τ) and ensure consistent formatting.
Unexplained abbreviations make the table difficult for readers to interpret.
15.
LOWreporting
Discuss the biological relevance of the HOMO-LUMO gap and ionization potential/electron affinity in the context of reactivity, and explicitly state that the reported positive values for IP and EA are taken as absolute values from negative orbital energies.
The sign convention for IP and EA is currently implicit and could confuse readers unfamiliar with computational conventions.

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