Journal of Molecular Structure Submission Guide
A package-readiness guide to the Journal of Molecular Structure: the experiment-plus-interpretation acceptance model, the Editorial Manager portal, the $3,190 hybrid APC, and the scope traps that send crystallography and DFT manuscripts back before review.
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How to approach Journal of Molecular Structure
Use the submission guide like a working checklist. The goal is to make fit, package completeness, and cover-letter framing obvious before you open the portal.
Stage | What to check |
|---|---|
1. Scope | Confirm structure-plus-interpretation scope versus Acta Crystallographica E and Journal of Molecular Modeling |
2. Package | Anchor the study with an experimental method and add interpretation that ties the structure to a chemical conclusion |
3. Cover letter | Prepare the editable source file, highlights, graphical abstract, CIF and CCDC number, and declarations |
4. Final check | Submit through Editorial Manager for the editor desk screen |
Quick answer: The Journal of Molecular Structure publishes new structural information that is interpreted, not just reported. The Elsevier journal runs single-anonymized review through Editorial Manager, carries a 4.7 impact factor and 8.0 CiteScore, and offers an optional $3,190 gold open-access APC on a hybrid model. Community acceptance estimates are directional rather than official publisher facts. The desk screen rewards structure plus interpretation, so the manuscripts that clear it are the ones that turn a crystal structure, a vibrational spectrum, or a DFT calculation into a chemical argument rather than stopping at the determination.
This Journal of Molecular Structure submission guide focuses on the real risk, which is not that your data is wrong. The journal's bar is technical, but its sharpest filter is scope. It rejects crystal-structure-only papers, docking-without-biochemical-confirmation papers, and purely theoretical studies by name in its own guide for authors. Before you spend the submission, use the Journal of Molecular Structure scope and readiness check to test whether your structure carries enough complementary analysis to clear the screen.
From our manuscript review practice
In our pre-submission review work with Journal of Molecular Structure manuscripts, the fastest desk rejections are not weak science. They are technically clean crystal structures, spectra, or DFT runs that stop at the data and never interpret it. The journal rejects crystal-structure-only papers and docking-without-confirmation papers by name, so a determination with no complementary analysis is a more common return here than a flawed experiment.
What does the Journal of Molecular Structure actually publish?
The Journal of Molecular Structure is realistic when three things are already true: the work reports genuinely new structural information, that structure is interpreted into a chemical conclusion, and an experimental result anchors the study. If the paper is a determination without an argument, or a calculation without an experiment, the portal will not rescue it.
What to pressure-test | What should already be true before upload |
|---|---|
Structural novelty | The paper reports new structural information on a molecule, intermediate, complex, or polymer, not a re-determination of a known structure. |
Interpretation | The structure is used to make a chemical point (bonding, conformation, intermolecular interactions, structure-property link), not just deposited and described. |
Experimental anchor | At least one experimental method (X-ray, IR, Raman, NMR, UV-Vis) underpins the work; pure DFT goes elsewhere. |
Scope | The molecular structure is the contribution, not a thin structural appendix on a materials, device, or bioactivity study. |
Declarations | Cover letter, highlights, graphical abstract, data availability, competing interest, CRediT, and ORCID are ready before upload. |
The Journal of Molecular Structure is Elsevier's long-running venue (since 1968) for structural information on all types of chemical species: stable and unstable molecules in any environment (vapour, solution, liquid crystal, solid state, matrix-isolated, surface-adsorbed), chemical intermediates, excited-state molecules, biochemicals, and polymers. The toolbox it expects is broad: X-ray crystallography, vibrational spectroscopy (IR and Raman), NMR, UV-Vis, and DFT or other computation used alongside experiment.
The acceptance criterion is worth internalizing before you write the cover letter. The journal states that papers "combining experimental and theoretical approaches to a problem are particularly welcomed," and it draws a hard line on the inverse: "solely theoretical (semiempirical or ab initio) studies should be submitted to the Journal of Molecular Structure: THEOCHEM." So the editor is not asking "is this structure correct?"
The editor is asking "does this structure, anchored by experiment, teach us something chemical?" That is a different question, and it is the one most authors under-prepare for because they optimized for the determination, not the interpretation.
What does the Journal of Molecular Structure submission portal require?
Journal of Molecular Structure manuscripts are submitted through Editorial Manager at editorialmanager.com/molstruc. The system handles upload, peer-review tracking, and revision. Here is what the initial submission needs to be complete.
Manuscript file and format: Submit a single editable file in Word (.docx) or LaTeX (.tex). The journal is explicit that "PDFs are not acceptable as source files," so a PDF-only upload is a common intake return. Figures may sit in the manuscript body for the refereeing version; the journal only requires the correctly formatted final files at the revision stage.
Abstract, highlights, and graphical abstract: Keep the abstract to roughly 250 words, supply 3 to 5 highlights of no more than 85 characters each, and include one graphical abstract image. Individual figure files are accepted up to 50 MB through Editorial Manager, so high-resolution spectra and packing diagrams do not need to be downsampled at submission. A missing graphical abstract is one of the most frequent return-for-correction triggers at intake, so prepare all three before you start the submission rather than during it.
Article types: The journal publishes full-length research articles and review papers. Reviews should be substantive surveys with structural focus, not short opinion pieces. Know which type you are submitting before you write, because the expectation for breadth and reference depth differs sharply between them.
Required declarations: Every submission needs a cover letter, a declaration of competing interest, a data availability statement, a CRediT author-contributions statement, and ORCID iDs for the corresponding author. An ethics approval statement is required for any human or animal work, and supplementary information should carry the crystallographic information files (CIF), spectra, and extended computational details that do not fit the main text. For X-ray work, the CIF and structure-factor files belong in the submission, and a deposited CCDC number is expected.
What is the Journal of Molecular Structure editorial triage timeline?
The Journal of Molecular Structure runs a fast desk screen and a standard two-reviewer process. Community-reported SciRev data suggests an immediate-rejection window of about 17 days, an acceptance estimate near one-third, and a meaningful share of submissions rejected without review. Treat those as directional planning signals, not publisher promises.
Day 0: Submission and intake
Editorial Manager accepts the package and runs format and completeness checks: editable source file, highlights, graphical abstract, declarations, and CIF for crystallographic work. Format-incomplete packages are returned here before an editor reads the science.
Days 1 to 17: Editor desk screen
A handling editor evaluates scope and structural contribution. This is where the journal's named out-of-scope rules bite: crystal-structure-only papers, docking-without-confirmation papers, and purely theoretical submissions are returned in this window. The reported immediate-rejection time clusters around 17 days, and roughly 18% of submissions never reach review.
Weeks 3 to 10: Single-anonymized peer review
Manuscripts that clear the desk screen go to a minimum of two reviewers who see author identities while staying anonymous themselves. Reviewers assess structural rigor, the validity of spectral or crystallographic assignments, and whether the interpretation is supported by the data.
Weeks 10 to 16: Decision and revision
Reject, major revision, minor revision, or accept. Major or minor revision is the most common outcome for in-scope manuscripts, and the journal usually runs one to two rounds before a final decision.
Weeks 16 to 18: Acceptance and production
Once accepted, authors supply correctly formatted final files. Subscription publication is free; authors who chose gold open access are invoiced the APC at this stage before the article publishes.
What slows a decision here
Two things drag out the JMS timeline more than reviewer availability. The first is a PDF-only or non-editable source file, which bounces at intake before an editor sees it. The second is a missing CIF or CCDC deposition number on a crystallographic paper, which stalls the manuscript in a check-and-return loop even when the science is sound. Both are avoidable in five minutes and both are slower to fix after submission than before it.
How does the Journal of Molecular Structure compare with its peer journals?
The Journal of Molecular Structure competes with several venues a structural chemist actually weighs. The editorial difference is not the citation metric, it is what each journal treats as a complete contribution. Note that JMS positions itself against flagship chemistry venues such as JACS and Angewandte Chemie only on scope, not selectivity; an author choosing among PNAS-adjacent breadth journals is in a different decision than one choosing among these structural specialists.
Journal | What it treats as a complete paper | Primary technique | JIF (2024) | APC model |
|---|---|---|---|---|
Journal of Molecular Structure | New structure PLUS interpretation, experiment-anchored | X-ray, IR/Raman, NMR, DFT (combined) | 4.7 | Hybrid, $3,190 OA optional |
Spectrochimica Acta Part A | Electronic/vibrational/rotational spectroscopy | Optical spectroscopy | ~4.3 | Hybrid |
Acta Crystallographica E | A crystal structure determination on its own | Single-crystal X-ray | ~0.5 | Fully open access |
CrystEngComm | Crystal design and engineering, not single structures | Crystal engineering | ~3.1 | Hybrid |
Journal of Molecular Modeling | Theoretical/computational molecular modeling | DFT and simulation | ~2.1 | Hybrid |
Source: JCR 2024 metrics, SCImago, and the journals' own scope and author pages (accessed June 2026).
The decision logic is editorial, not numeric. Choose the Journal of Molecular Structure when you have new structural data AND a chemical interpretation that ties it together. Choose Acta Crystallographica E when your contribution genuinely is the crystal structure itself, which is precisely the paper JMS rejects as out of scope; this is the single most useful re-routing for authors whose work bounces from JMS.
Choose Spectrochimica Acta Part A when the spectroscopy is the contribution rather than a supporting characterization. Choose CrystEngComm when the story is crystal design or supramolecular engineering rather than one molecule's structure. Choose Journal of Molecular Modeling when the work is purely computational with no experimental anchor, the same case JMS sends to THEOCHEM.
The mistake we see most is authors picking JMS on the citation metric and getting desk-rejected for scope, when a crystal-structure-only paper would have been accepted at Acta E in weeks.
For deeper context on the closest peers, see is RSC Advances a good journal, is Scientific Reports a good journal, and the Molecules submission guide.
Common rejection triggers at the Journal of Molecular Structure
In our pre-submission review work with Journal of Molecular Structure manuscripts, the desk-screen failures cluster around interpretation and scope, not around whether the data is correct. Because the journal rejects several manuscript shapes by name in its own guide for authors, the patterns that send chemistry papers back are unusually predictable, and each is a specific, named rejection pattern you can test against your own draft before you upload.
Across our Journal of Molecular Structure pre-submission reviews, four patterns generate the most consistent early returns. In our review of structural chemistry manuscripts deciding among JMS, Acta Crystallographica E, and Journal of Molecular Modeling, the same editorial triage repeats: editors screen scope and interpretation before they assess the science itself.
How this guide was built: we reviewed the Journal of Molecular Structure's published guide for authors and its stated out-of-scope rules, and the sources checked are listed at the end of this page. Our Manusights submission analysis then compared those guidelines with recurring patterns across 40 manuscripts we reviewed for these structural-chemistry venues, where the scope-mismatch pattern was the most common, a finding consistent with the journal's own immediate-rejection rate near 18% reported on SciRev.
A Manusights review checks whether your paper clears the JMS-specific scope and interpretation tests that a generic author checklist cannot evaluate. Paid Manusights reviews include a 60-day money-back guarantee, and we do not train models on submitted manuscripts.
Crystal structure reported as the sole result
The single most common Journal of Molecular Structure desk-screen trigger we see is a crystal-structure-only paper. The journal states plainly that it will not consider "studies reporting crystal structures as the main or sole result, without significant complementary analysis or interpretation." A manuscript that determines a structure, tabulates bond lengths and angles, draws the packing diagram, and stops there reads as a structural communication, not a structural study.
The fix is interpretation: connect the geometry to a Hirshfeld surface analysis, a vibrational assignment, a structure-property relationship, or a comparison across a family of compounds. If the contribution genuinely is the structure itself, the correct home is Acta Crystallographica E, and a fast acceptance there beats a slow rejection here.
Check whether your Journal of Molecular Structure paper has enough complementary analysis
Docking results with no biochemical confirmation
A second named pattern is the docking add-on. The journal explicitly excludes "studies reporting crystal structures along with only docking results but no biochemical confirmation." Authors who determine a small-molecule structure and then dock it into a protein to suggest a binding mode, without any assay, enzyme inhibition data, or biological validation, are reporting a computational hypothesis dressed as a result.
To an editor screening for structural substance, an unvalidated docking section actively weakens the paper rather than strengthening it. Either supply the biochemical confirmation, or cut the docking and let the structural chemistry stand on its own.
Purely theoretical work with no experiment
A third recurring failure is the DFT-only submission. The guide is unambiguous: "solely theoretical (semiempirical or ab initio) studies should be submitted to the Journal of Molecular Structure: THEOCHEM." A paper that optimizes a geometry, computes frequencies, and reports HOMO-LUMO gaps and molecular electrostatic potential maps with no measured spectrum or diffraction data is out of scope at the parent journal regardless of how careful the calculation is.
The journal welcomes theory that supports experiment; it rejects theory that stands alone. If there is no experimental anchor, the Journal of Molecular Modeling or THEOCHEM is the right venue, not this one.
Scope drift into materials or bioactivity
The fourth pattern is the thin structural wrapper. The journal excludes "studies dealing with glasses, particles and other materials with little content about molecular structure," and work "focusing on synthesis procedures or evaluation of bioactivity of molecules without significant relationship with molecular structure."
A manuscript whose real contribution is a nanoparticle's catalytic performance, a device's efficiency, or a compound's IC50, with a token X-ray or IR section bolted on, reads as out of scope to a structure editor. The test is simple: if the central hypothesis is not a molecular-structure hypothesis, the scope fit is weak no matter how much characterization data the supplementary file contains.
Run a Journal of Molecular Structure desk-screen check before you submit
Submit If
The Journal of Molecular Structure is the right home for a wide band of experiment-anchored structural chemistry. Submit when these specific, testable conditions hold:
- the paper reports genuinely new structural information and uses it to make a chemical argument, not just to deposit a determination
- at least one experimental method (single-crystal X-ray, IR, Raman, NMR, or UV-Vis) underpins the study, with theory used in support rather than alone
- any docking or computational section is backed by experimental or biochemical confirmation, not presented as a standalone result
- the molecular structure is the contribution, and crystallographic work includes the CIF, structure factors, and a CCDC deposition number
The review tells you whether YOUR paper passes the JMS scope and interpretation screen before you upload, not just what the guidelines say in the abstract.
Think Twice If
The Journal of Molecular Structure is not the right venue for everything. Pause if any of these specific manuscript patterns describe your draft:
- the paper determines a crystal structure and stops at bond lengths, angles, and a packing diagram with no complementary analysis (route this to Acta Crystallographica E instead)
- the only link to biology is a docking study with no assay or biochemical confirmation
- the work is purely DFT or ab initio with no measured spectrum or diffraction data (THEOCHEM or the Journal of Molecular Modeling is the correct home)
- the real contribution is a material's property, a device's performance, or a compound's bioactivity, with a thin structural section attached to qualify for the journal
If you are unsure which side of the line your draft falls on, run a Journal of Molecular Structure manuscript fit check to surface the scope and interpretation gaps before an editor does. The check is free to run (/ai-review) and takes a single upload.
What is the Journal of Molecular Structure pre-submission checklist?
- [ ] The paper reports new structural information AND interprets it into a chemical conclusion
- [ ] At least one experimental method anchors the study;
any DFT supports rather than replaces experiment
- [ ] Crystallographic work includes the CIF, structure factors, and a CCDC deposition number
- [ ] Any docking or computational binding claim is backed by biochemical confirmation
- [ ] The manuscript is an editable Word or LaTeX file, not a PDF source
- [ ] 3 to 5 highlights (85 characters each), a graphical abstract, competing-interest declaration, data statement, CRediT, and ORCID are ready
- [ ] You have decided whether to publish by subscription (free) or pay the $3,190 open-access APC
- ] Run a final [Journal of Molecular Structure submission readiness check to catch the scope gaps editors filter for on first read
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What should you read next?
Frequently asked questions
The Journal of Molecular Structure (Elsevier) accepts work that delivers new structural information AND a real interpretation of it. A crystal structure, a spectrum, or a DFT calculation on its own is not enough; the paper has to use the structure to say something chemical. Review is single-anonymized with a minimum of two reviewers. Community-reported SciRev data suggests an immediate-rejection window of about 17 days and an acceptance estimate near one-third, with a meaningful share of submissions rejected without review; treat those figures as directional, not publisher promises.
The journal explicitly will not consider: crystal structures reported as the main or sole result without significant complementary analysis or interpretation; crystal structures paired only with docking results and no biochemical confirmation; purely theoretical (semiempirical or ab initio) studies with no experimental results; materials and particle studies with little molecular-structure content; and work on commercially available compounds that brings no significant novelty. Solely theoretical work belongs in THEOCHEM, not here.
Submit through Editorial Manager at the official submission portal as a single editable Word (.docx) or LaTeX (.tex) file; PDF is not an acceptable source file. The package needs a cover letter, 3 to 5 highlights of 85 characters each, a graphical abstract, a declaration of competing interest, a data availability statement, CRediT author contributions, and ORCID. A missing graphical abstract is a common return-for-correction at intake.
The Journal of Molecular Structure is a hybrid journal. Publishing by subscription is free to the author; choosing gold open access carries an Article Publishing Charge of $3,190 USD excluding tax. Open access is optional, so authors who do not need it can publish at no charge. Check whether your institution has an Elsevier read-and-publish agreement that covers the APC before you opt in.
Yes. The Journal of Molecular Structure is published by Elsevier, has run since 1968, and is indexed in Web of Science and Scopus. The current Elsevier journal page lists a 4.7 impact factor and 8.0 CiteScore. It is a long-established, high-volume venue for experimental-plus-interpretive molecular structure work, not a predatory journal.
Sources
- Journal of Molecular Structure guide for authors (ScienceDirect)
- Journal of Molecular Structure Editorial Manager submission portal
- Journal of Molecular Structure open-access options (ScienceDirect)
- Journal of Molecular Structure metrics (Researcher.Life)
- Journal of Molecular Structure review-process data (SciRev)
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