Is Your Paper Ready for Molecules? MDPI's Broad Chemistry Journal

The 4.6 IF deserves some context. That's higher than many researchers expect for a journal with this acceptance rate and volume. It's driven partly by the sheer number of papers Molecules publishes (more papers means more citation opportunities within the journal), partly by the broad scope (cross-disciplinary work gets cited from multiple communities), and partly by special issues that sometimes generate themed citation clusters. It's a real IF, but it doesn't mean Molecules is editorially equivalent to a journal like Journal of Medicinal Chemistry (IF ~7) or ACS Catalysis (IF ~12) that achieves a similar or higher number through more selective editorial standards.

You can't write honestly about Molecules without addressing MDPI's reputation, so let's not pretend this isn't on your mind.

MDPI publishes hundreds of journals at enormous scale. The business model depends on article processing charges and high volume. The special issue system generates thousands of themed collections, some with excellent guest editors and some with guest editors who aren't particularly active in the field. Review turnaround times are fast enough that experienced researchers sometimes wonder how thorough the process really is. And in certain departments, particularly in parts of Europe, MDPI publications are treated with open skepticism during hiring and promotion reviews.

Here's what's also true: Molecules has been around since 1996. It's indexed in Web of Science, Scopus, and PubMed. It hasn't been dropped from any major index. The papers in it go through peer review, and plenty of them are perfectly sound chemistry. MDPI follows COPE guidelines and isn't listed on any credible predatory publisher database.

The practical question isn't whether Molecules is "legitimate" in some abstract sense. It clearly is. The question is whether your specific department, your specific hiring committee, or your specific grant review panel treats MDPI publications differently than publications in, say, ACS or RSC journals. If you don't know the answer, ask a senior colleague in your department before you submit. This isn't something you want to discover after the paper is already published.

Molecules runs a large number of special issues at any given time. This is standard MDPI practice, and it's worth understanding because many Molecules submissions come through special issue invitations rather than the regular submission track.

Here's how it works. A guest editor proposes a themed collection to MDPI. If approved, the guest editor recruits submissions, often by emailing researchers directly. Papers submitted to the special issue go through peer review, with the guest editor handling editorial decisions. The papers are published individually as they're accepted, then grouped into the special issue collection.

When this works, it's genuinely useful. A well-curated special issue on, say, "Recent Advances in Flavonoid Chemistry" led by a recognized phytochemist can produce a focused, well-cited collection. The guest editor brings expertise, the topic is specific enough to attract relevant work, and the resulting collection becomes a reference point for that subcommunity.

When it doesn't work, you get a loosely themed collection with papers that wouldn't have been written if the invitation hadn't arrived. The guest editor is a name on the masthead but isn't actively shaping the collection. The topic is so broad ("New Frontiers in Organic Chemistry") that the papers have nothing in common beyond existing.

Before accepting a special issue invitation, ask yourself three things. First, would you have written this paper anyway, or are you writing it because someone emailed you? Second, is the guest editor someone whose opinion you'd actually value during review? Third, is the special issue topic specific enough that your paper belongs alongside the others?

Regular submissions to Molecules go through the same peer review process without the special issue framing. There's nothing wrong with the regular track, and it avoids some of the perception issues that special issues can carry.

You're working in a chemistry subfield with limited journal options. Natural products chemistry, food chemistry, and phytochemistry don't have as many dedicated journals as organic synthesis or catalysis. Molecules is a primary venue for these areas, and papers in these subfields make up a large share of the journal's most-cited work. If your field publishes here regularly, there's no perception penalty.

Your paper is solid but incremental. You've synthesized a new series of compounds, tested their bioactivity, and the results are real but won't reshape the field. JACS isn't going to take this. ACS Medicinal Chemistry Letters probably won't either. Molecules will give it a fair review and publish it quickly if the chemistry is sound. There's nothing wrong with incremental science, and not every paper needs to be in a top-5 journal.

Speed matters. If you're finishing a PhD, wrapping up a project, or working on time-sensitive research that needs to be in the literature quickly, Molecules' 2-4 week decision time and 6-10 week publication timeline are hard to beat. Traditional chemistry journals can take 3-6 months just for a first decision. That time difference is real and it matters for careers.

Your grant covers the APC and you need an open access venue. Some funders require immediate open access. At $2,700, Molecules is cheaper than most ACS or RSC open access options. If your grant has publication funds earmarked and you need gold OA, Molecules is a practical choice.

You want PubMed indexing for a chemistry paper. Not all chemistry journals are indexed in PubMed. Molecules is. If your work has biomedical relevance and you want it discoverable through PubMed searches, that's a genuine advantage.

Molecules rejects more than half its submissions. Here's what goes wrong.

Characterization gaps. If you're reporting new compounds and the characterization data is incomplete (missing NMR assignments, no HRMS, inadequate purity evidence), reviewers will flag it immediately. Molecules doesn't require single-crystal X-ray for every compound, but the characterization standards are real. Don't submit with placeholder data expecting to fill it in during revision.

"Screening paper" syndrome. You've tested 30 compounds against 3 cell lines and are reporting IC50 values. That's fine as far as it goes, but if there's no SAR analysis, no mechanistic insight, and no comparison to known active compounds, the paper reads like a data dump. Reviewers want to know what the results mean, not just what they are.

Computational papers with no experimental validation. Molecules publishes computational chemistry, but reviewers are increasingly skeptical of molecular docking studies that predict binding affinities without any wet-lab confirmation. If your entire paper is in silico, you'll need an unusually thorough computational approach or you'll face requests for experimental data you can't provide.

Natural products papers that stop at isolation and identification. Isolating a known compound from a new source isn't enough on its own. Reviewers expect either a new compound, a new bioactivity, an improved isolation method, or some other element of novelty. "We found quercetin in this plant too" isn't a publishable finding.

Missing data availability statements. MDPI requires these, and the editorial office will send your paper back if it's missing. Prepare it before submission. If your data can be deposited in a public repository, do it. If it can't, explain why clearly.

Molecules uses MDPI's standard submission platform. A few things that'll save you time.

Use the MDPI template from the start. MDPI's formatting requirements are unusually specific. If you submit in a different format, the editorial office will return it for reformatting before review begins. Don't waste a week on this. Download the Word or LaTeX template and use it.

Get your compound characterization in order. For synthetic papers, every new compound needs full characterization: 1H and 13C NMR with complete assignments, HRMS, melting points for solids, and purity data. For natural products, include isolation yields and spectroscopic comparison to literature if the compound is known.

Write a real graphical abstract. MDPI journals display graphical abstracts prominently. A good one increases visibility. A generic ChemDraw scheme with an arrow pointing to "bioactivity" doesn't cut it. Show the actual result or the most interesting structural feature.

Don't ignore the cover letter. It doesn't need to be long, but it should explain why your paper fits Molecules specifically. If you're submitting to a special issue, mention which one and why your work is relevant to the collection.

Before submitting, running your manuscript through an AI-powered manuscript review can catch structural issues, missing data statements, and scope alignment problems that would otherwise slow you down during editorial screening.