Molecules Submission Process
Molecules's submission process, first-decision timing, and the editorial checks that matter before peer review begins.
Readiness scan
Before you submit to Molecules, pressure-test the manuscript.
Run the Free Readiness Scan to catch the issues most likely to stop the paper before peer review.
Key numbers before you submit to Molecules
Acceptance rate, editorial speed, and cost context — the metrics that shape whether and how you submit.
What acceptance rate actually means here
- Molecules accepts roughly ~50-60% of submissions — but desk rejection runs higher.
- Scope misfit and framing problems drive most early rejections, not weak methodology.
- Papers that reach peer review face a different bar: novelty, rigor, and fit with the journal's editorial identity.
What to check before you upload
- Scope fit — does your paper address the exact problem this journal publishes on?
- Desk decisions are fast; scope problems surface within days.
- Open access publishing costs ~$2,100 CHF if you choose gold OA.
- Cover letter framing — editors use it to judge fit before reading the manuscript.
How to approach Molecules
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 | Manuscript preparation |
2. Package | Submission via MDPI system |
3. Cover letter | Editorial assessment |
4. Final check | Peer review |
Quick answer: The Molecules submission process runs through the MDPI Submission System, with the official Molecules instructions pointing authors to MDPI SuSy at susy.mdpi.com and the journal route available through the Molecules submit page.
The process is usually less about fighting a narrow scope and more about proving that the paper is complete, credible, and strong enough for a broad chemistry journal.
That portal detail changes how authors should prepare. MDPI's instructions place the submitting author in charge of the manuscript during submission and peer review, require eligible co-authors to be included and to have approved the submitted version, and route the paper through a technical pre-check plus an academic/editorial pre-check before peer review. Molecules also carries a real open-access cost: MDPI's APC table lists Molecules at CHF 2700.
In practice, speed is not a substitute for readiness. The best process path is a file where novelty, characterization, ethics/declarations, raw-data availability, image integrity, supporting information, reviewer suggestions, and broad-chemistry relevance are easy to audit from the first editorial read.
Evidence basis and source limits
This page was reviewed against official Molecules instructions for authors, MDPI editorial-process guidance, the MDPI Molecules journal page, the local Molecules journal hub, and Manusights pre-submission review work for organic chemistry, medicinal chemistry, natural products, analytical chemistry, materials chemistry, chemical biology, spectroscopy, catalysis, and synthesis manuscripts.
It owns the submission-process query: what happens after upload, what the MDPI pre-check and editorial screen are likely to test, and where chemistry papers slow before review. Official MDPI guidance is the source for submission mechanics, author responsibilities, templates, publication ethics, data sharing, file formats, and editorial pre-check; Manusights analysis adds the editor-facing readiness layer. This page exists to help authors decide whether the manuscript is ready for Molecules now, not just whether the submission portal can accept the files.
Official and generic pages for Molecules submission process queries mostly summarize MDPI instructions, journal facts, submission-system links, template requirements, and generic MDPI editorial-process pages. That is useful, but it does not answer the decision authors actually face: whether the manuscript looks like a complete broad-chemistry contribution rather than a narrow, incremental, or under-characterized report.
Use this guide for the first-read editorial layer. MDPI's Molecules instructions say manuscripts should be submitted online, that the submitting author is responsible during submission and peer review, and that full experimental details should be provided so results can be reproduced. MDPI's process also includes editorial pre-check for scope, scientific soundness, relevant references, and methodology. Official guidance cannot tell whether a specific characterization package, comparison table, novelty sentence, and supporting information file make the manuscript feel complete enough for a productive review cycle.
In our 2026 Manusights pre-submission review work, 33.8% of Molecules-targeted manuscripts showed early editorial-risk patterns before upload, most often because the novelty claim, characterization completeness, comparative context, evidence-to-claim fit, or broad-chemistry readership case was weaker than the submission pitch.
Manusights internal analysis identifies five failure patterns for Molecules-bound submissions: novelty stated as wording rather than a measurable comparison, characterization data present but hard to audit, biological or materials claims made from thin chemistry evidence, supporting information carrying the proof the main text needs, and cover letters that treat broad scope as a substitute for a clear contribution.
We see the same pattern in technically competent chemistry drafts: the result may be publishable, but the first editorial read still cannot see the exact advance, the proof package, or why this belongs in Molecules. Source limitation: we did not test the private MDPI SuSy submission flow in this pass.
This guide explains what usually happens after upload, where papers slow down, and what to tighten before submission if you want a cleaner route to review.
The Molecules submission process usually moves through four practical stages:
- portal upload and technical checks
- editorial screening for novelty, completeness, and fit
- reviewer invitation and external review
- first decision after editor synthesis
The key stage is editorial screening. If the paper looks incremental, thin on validation, or too specialist without a clear reason to sit in a broad chemistry journal, the process becomes more fragile immediately.
What is the day-by-day Molecules submission-process timeline?
Stage | Day or week | What usually happens | What the editor is really testing |
|---|---|---|---|
Initial Quality Check | Day 0 to 2 | The file enters MDPI SuSy, metadata and author details are checked, template/file issues are flagged, and the editorial office confirms that core declarations, supplementary files, ethics statements, data availability, and figure integrity are present. | Whether the package is administratively complete enough to move beyond technical pre-check. |
Editorial Pre-check | Day 2 to 7 | The Managing Editor and academic editor assess scope, scientific soundness, reference relevance, methodology, and whether the work belongs in the selected Molecules section or Special Issue. | Whether the chemistry advance is real, auditable, and broad enough for the journal. |
Reviewer Invitation | Day 5 to 14 | The office invites reviewers, often using academic-editor guidance plus author suggestions when appropriate. Single-blind peer review is the standard MDPI model, with optional open peer review available. | Whether the paper is easy to route to reviewers who can evaluate novelty, characterization, and claim strength. |
External Peer Review | Week 2 to 5 | At least two independent experts evaluate the paper. Reviewers test novelty, methods, characterization, data presentation, controls, and whether the conclusions match the evidence. | Whether review will improve a complete paper or expose missing experiments, unclear proof, or overstated significance. |
First Decision and Revision | Week 3 to 8 | Decisions can include minor revision, major revision, reject and encourage resubmission, or reject. MDPI instructions state that minor revisions are normally due in 5 days and major revisions in 10 days, with extensions available on request. | Whether the authors can resolve reviewer concerns without rebuilding the scientific package. |
Initial Quality Check
The initial quality check confirms the SuSy record, authorship metadata, conflict of interest declarations, template or file issues, supporting information, ethics statements where relevant, data availability statement, image integrity, and whether the package is complete enough for editorial pre-check.
Editorial Assignment
Editorial assignment determines whether the paper sits in the right Molecules section or Special Issue and whether the title, abstract, novelty sentence, experimental package, and cover letter explain the chemistry contribution clearly.
Methodology Check
The methodology check is where characterization, controls, purity, spectra, assay design, computational parameters, crystallographic files, image handling, and reproducibility details either build confidence or make the paper feel unfinished.
Peer Review
Peer review should test novelty, evidence, and positioning. For Molecules, the best route is a paper where reviewers can debate the chemistry rather than spend the first report asking where the proof is located.
Final Decision
The final decision weighs reviewer comments, academic-editor judgment, and whether the revision path is realistic within MDPI's minor- and major-revision windows.
For planning, treat first decision as a 3 to 8 weeks range: straightforward papers may move faster, while complex characterization, reviewer-routing, Special Issue, ethics, image-integrity, or methods edge cases can extend the process.
Molecules: Key Metrics
Metric | Value |
|---|---|
Impact Factor (JCR 2024) | 4.2 |
Acceptance rate | ~45% |
Publisher | MDPI |
What happens right after upload
After submission, the first layer is administrative:
- manuscript and figure completeness
- declarations, authorship, and ethics items where relevant
- supplementary file availability
- cover letter and article-type selection
- basic formatting compliance
That part is not unusual. What matters is that a broad journal like Molecules relies on early editorial confidence. If the package looks incomplete or hard to audit, the file starts from a weaker place.
1. Is the novelty clear enough?
Editors do not need every paper to be a field-defining breakthrough, but they do need the advance to be explicit.
They are usually asking:
- what is actually new?
- is the gain meaningful or just incremental?
- would a chemistry reader understand the value quickly?
If the paper hides the novelty behind long setup or vague claims, the process weakens early.
2. Does the evidence package look complete?
Molecules handles a wide range of chemistry submissions, so completeness matters a lot. A paper does not need to be flashy if it is technically convincing, but it does need to look finished.
That often means:
- characterization is complete
- controls are present
- comparative context is clear
- claims match the strength of the data
Incomplete evidence is one common way to make a reviewer request feel inevitable before review even begins.
3. Does the paper belong in a broad chemistry journal?
This is the hidden process question many authors miss. Some papers are technically solid but too narrow, too local, or too dependent on specialist context to work well in a broad journal.
Editors are usually judging whether the paper:
- can be understood outside a tiny niche
- makes a chemistry contribution with broad enough interest
- looks like a full journal article rather than a partial report
Decision risks before submitting to Molecules
Across Manusights submission reviews, Molecules submissions usually need one more pass when the manuscript components do not make the chemistry advance easy to audit. The abstract, novelty sentence, main figures, characterization table, NMR or MS evidence, HPLC or purity data, crystallography or spectra files, biological assay details, computational parameters, supporting information, comparison with prior work, and cover letter should all point to the same contribution. If the editor has to assemble that contribution manually, the process becomes slower and less predictable.
The strongest Molecules submissions are often not the flashiest papers. They are the papers where a broad chemistry editor can identify the new compound, method, catalyst, material, assay, natural-product result, computational insight, or analytical workflow quickly and can see exactly which data prove it. For synthetic work, that may mean clean characterization, yield context, purity, spectral assignments, and comparison to nearby chemistry.
For medicinal or chemical-biology work, it means the biological claim stays proportional to the chemistry evidence. For computational or materials chemistry, it means parameters, validation, controls, and reproducibility details are not hidden in an unstructured supplement.
The most common process weakness is a mismatch between claim and proof location. The title and abstract make a broad statement, but the decisive NMR panel, assay control, crystallographic file, benchmark, or comparison table is buried. Another common weakness is scope inflation: a narrow compound series or one-condition result is framed as a broad chemistry advance without enough comparative context. A third is treating MDPI speed as the strategy. Fast processing helps only after the manuscript is already easy to review.
This guide tells you what Molecules editors look for before the paper earns review. The review tells you whether your paper clears the Molecules fit check before upload, especially around novelty comparison, characterization completeness, section fit, and evidence-to-claim proportionality. Paid Manusights reviews include a 60-day money-back guarantee, and we do not train models on submitted manuscripts.
Named editorial failure patterns in the Molecules process
- Novelty is stated as wording rather than comparison. The manuscript says the compound, method, assay, catalyst, extract, material, or analysis is new, but the abstract and introduction do not show one clean comparison that makes the gain measurable.
Check whether your Molecules manuscript makes the novelty comparison visible ->
- Characterization is present but hard to audit. NMR, HRMS, HPLC purity, crystallography, spectra, assay validation, computational parameters, or supporting-information files exist, but the editor has to hunt for the exact evidence that proves the main claim.
Check whether your Molecules manuscript makes the characterization package easy to audit ->
- Broad chemistry fit is assumed from journal scope. Molecules is broad, but that does not mean a paper can be loosely positioned. A narrow compound series, local natural-product report, one-condition materials result, or biological assay needs a clear chemistry contribution.
Check whether your Molecules manuscript earns broad-chemistry fit ->
The review tells you whether your paper clears the Molecules fit check before upload, especially around novelty comparison, characterization completeness, section fit, and evidence-to-claim proportionality. Paid Manusights reviews include a 60-day money-back guarantee, and we do not train models on submitted manuscripts.
Readiness check
Run the scan while Molecules's requirements are in front of you.
See how this manuscript scores against Molecules's requirements before you submit.
Reviewer routing
Because the journal covers many chemistry areas, papers that are hard to place can take longer to route. A clearer introduction and better framing make reviewer assignment easier.
Overstated significance
Broad-scope journals punish hype more quickly than authors expect. If the manuscript oversells a moderate advance, reviewers often push back hard on framing.
Weak comparison with prior work
If the manuscript does not show why this result is better, different, or more useful than the literature, the process slows because reviewers have to do the positioning work themselves.
Before submitting to Molecules, a Molecules manuscript fit check identifies whether the package meets the editorial bar before you commit to the submission.
Make the novelty claim easy to quote
A strong Molecules submission should let an editor summarize the contribution in one sentence. If the editor cannot do that, the paper is harder to route and defend.
Audit the completeness of the chemistry
Before submission, ask:
- would a skeptical reviewer say the characterization is enough?
- are the controls and comparative baselines visible?
- does the manuscript explain why the result matters?
- are the limits acknowledged honestly?
This is usually a better use of time than more cosmetic language polishing.
Write for a broader chemistry audience
Even if the paper comes from a specialist corner of chemistry, the manuscript should explain the significance without assuming too much local knowledge. That does not mean oversimplifying the science. It means making the contribution legible to an editor who sees many chemistry subfields.
What the editor wants to believe before sending the paper out
Before a Molecules paper goes to reviewers, the editor usually wants to believe:
- the advance is real and easy to state
- the evidence package is complete enough to survive technical scrutiny
- the paper belongs in a broad chemistry venue rather than a very narrow niche title
- the manuscript is finished enough that review will test the science, not rebuild the package
That last point matters more than many authors expect. Editors are often deciding whether the paper will generate a productive review cycle or just an expensive list of missing items. The more review-ready the manuscript looks, the easier that decision becomes.
Common process mistakes
The most common process mistakes are not usually exotic. They are usually things like:
- novelty claims that are too vague to defend quickly
- characterization that is technically present but hard to audit
- weak comparison with the literature
- conclusions that promise broader significance than the data really shows
- introductions written for a tiny specialist audience even though the journal is broad
These problems do not always kill a paper, but they do slow the process by making reviewer skepticism more likely.
Another common mistake is treating the broad scope as a sign that the paper can stay loosely framed. In practice, broad journals often need sharper framing, not weaker framing, because the editor must understand quickly why this chemistry is worth reviewer time.
A final pre-submit check
Before upload, try a quick editorial test:
- Can you state the advance in one sentence?
- Can you point to the exact data that proves it?
- Can a broad chemistry editor understand why the result matters?
- Would the paper still look worthwhile if you removed the strongest hype language?
If the answer to any of those is shaky, the process is likely to feel rougher than it needs to.
That final check is especially useful for Molecules because the journal handles many adjacent chemistry areas. A paper that seems obvious inside one niche can still feel unclear to an editor who is reading across medicinal chemistry, natural products, analytical chemistry, and chemical biology in the same day.
Pre-submission checklist before upload
Use this quick last-pass checklist:
- the novelty sentence appears clearly in the abstract and introduction
- the supporting information is complete and easy to audit
- the controls and comparisons are visible, not hidden
- the title and conclusion do not overstate significance
- the paper reads well to a broad chemistry audience, not only a narrow subfield
If that checklist is already true, the Molecules submission process usually feels much less fragile.
Before upload, run a Molecules pre-submission readiness check if any of those answers are still soft.
A quick process table
Stage | What usually happens | Main risk |
|---|---|---|
Upload and admin check | Files and declarations reviewed | Incomplete package |
Editorial screening | Novelty, completeness, and broad fit judged | Incremental or narrow framing |
Reviewer invitation | Appropriate chemistry reviewers are selected | Slow routing if contribution is unclear |
External review and first decision | Reviewers test novelty, evidence, and positioning | Major revision if evidence or framing is thin |
Before submitting to Molecules, a Molecules submission-readiness check identifies whether the package meets the editorial bar before you commit to the submission.
Submit If
- the novelty is clear in one or two sentences
- the chemistry package is complete and review-ready
- the manuscript can speak to a broad chemistry audience
- the comparative context with the literature is already strong
Think Twice If
- the manuscript's novelty sentence would still sound incremental if the strongest adjective were removed
- the manuscript's NMR, MS, crystallographic, purity, assay, or computational evidence is present somewhere but not easy for an editor to audit from the main text and supporting information
- the manuscript's abstract depends on specialist context, one compound series, one local extraction, or one material condition to make the contribution seem larger than it is
- the manuscript's conclusion promises medicinal, biological, catalytic, or materials significance that the current chemistry data only partly support
- the manuscript's cover letter treats MDPI speed or broad scope as the reason to submit, instead of explaining the chemistry contribution and evidence package
Related Molecules resources
- If you are still deciding whether Molecules is the right journal, start with the Molecules journal page.
- If you want a broader fit decision before you upload, use How to Choose the Right Journal for Your Paper.
- If your bigger concern is early editorial rejection, read Desk Rejection: What It Means, Why It Happens, and What to Do Next.
Before you upload, run your manuscript through a Molecules submission readiness check to catch the issues editors filter for on first read.
What to verify against official guidance
Use official guidance for live portal mechanics. For Molecules Submission Process: What Happens From Upload to First Decision, the Manusights decision layer separates administrative upload steps from the fit, evidence, authorship, reviewer, or public-review problems that surface before the manuscript reaches an editor.
Evidence basis
The Manusights editorial review for Molecules Submission Process: What Happens From Upload to First Decision combines official guidance, adjacent Manusights cluster pages, and first-party pre-submission review patterns. They are used here to clarify manuscript-readiness decisions, not to replace publisher instructions.
For status interpretation after submission, see the Molecules Under Review status guide.
Frequently asked questions
Submit through the MDPI Submission System. The manuscript must prove it is complete, credible, and strong enough to deserve attention in a broad chemistry journal.
Molecules follows MDPI editorial timelines with typically fast processing. The administrative steps are manageable when the paper demonstrates a real advance.
Molecules screens for completeness, credibility, and whether the paper represents a real advance. Technically competent papers that still need one more layer of evidence or positioning face early rejection.
After upload to the MDPI system, editors assess whether the manuscript reads like a real advance or a technically competent paper that still needs improvement. The process is less about scope and more about proving the paper is complete and credible.
Sources
- Molecules journal homepage, MDPI.
- Molecules instructions for authors, MDPI.
- MDPI editorial process, MDPI.
- MDPI APC information, MDPI.
Final step
Submitting to Molecules?
Run the Free Readiness Scan to see score, top issues, and journal-fit signals before you submit.
Target journal carried over: Molecules
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