Is Molecules a Good Journal? Reputation, Fit and Who Should Submit

Here's the elephant in the room. MDPI has faced criticism over predatory publishing practices, aggressive marketing tactics, and rapid expansion across hundreds of journals. Some academics view the entire MDPI portfolio with skepticism.

But Molecules predates most of these concerns. It launched in 1996, long before MDPI's expansion spree, and maintains legitimate peer review standards. The journal requires 2-3 reviewers with documented expertise, provides detailed reviewer reports, and rejects papers for insufficient data or poor experimental design.

The predatory journal accusations primarily target MDPI's newer, specialized titles, not established journals like Molecules. However, the association matters for career advancement. In conservative chemistry departments, publishing in any MDPI journal might raise eyebrows during tenure review.

This perception varies dramatically by institution and geography. European researchers often view MDPI more favorably than their American counterparts. Younger faculty may be more accepting than senior colleagues who remember traditional publishing models.

The open access model also affects perception. While many researchers appreciate immediate publication and broad readability, others associate author fees with pay-to-publish schemes. Molecules charges around $2,600 for publication, which some funding agencies cover but others don't.

Your career stage matters here. If you're a postdoc at a top-tier institution aiming for faculty positions at R1 universities, the MDPI association could be a liability. If you're an industry researcher or at a teaching-focused institution, it's rarely an issue.

The practical reality is that Molecules Impact Factor 2026: Ranking, Quartile & What It Means shows the journal maintains solid metrics despite publisher concerns. But perception often matters more than metrics in academic hiring.

Molecules' 4.6 impact factor places it in the middle tier of chemistry journals. It's respectable but not elite.

For context, Journal of Organic Chemistry sits at 3.6, making Molecules actually higher ranked in this specific comparison. Organic Letters commands 5.2, while Journal of Natural Products reaches 5.1. The medicinal chemistry space shows similar positioning, with Journal of Medicinal Chemistry at 7.3 and Bioorganic & Medicinal Chemistry at 3.5.

The 4.6 IF reflects Molecules' broad scope and practical focus. Papers don't need breakthrough novelty to get cited, just solid experimental work that other researchers can build on. This makes citation accumulation more predictable than in high-impact journals where papers either explode or disappear.

The journal sits in Q2 in both Organic Chemistry and Biochemistry & Molecular Biology categories. Not top quartile, but solidly respectable for most career purposes.

Don't mistake Molecules' 50-60% acceptance rate for low standards. The journal rejects plenty of papers, just not for the same reasons as Nature Chemistry.

Common rejection reasons tell the real story. Insufficient characterization data kills more submissions than anything else. Submit a new compound without 13C NMR, proper mass spectrometry, or elemental analysis, and you're getting rejected regardless of synthetic novelty.

Bioactivity papers face different hurdles. Reviewers expect dose-response curves, not single-point screening data. They want positive controls, cytotoxicity assessments, and proper statistical analysis. A paper claiming "compound X shows anticancer activity" based on one cell line at one concentration won't survive peer review.

The review process typically involves specialists in synthetic methodology or biological evaluation, depending on your paper's focus. These reviewers know the literature and spot overclaimed advantages quickly. Saying your synthetic route is "more efficient" requires actual yield comparisons and substrate scope data.

Methodological papers need rigorous benchmarking against existing procedures. Claiming improved conditions means demonstrating those improvements across multiple substrates, not just the best example.

The acceptance rate reflects the journal's scope-based editorial philosophy rather than low standards. Papers get accepted if they meet technical requirements and provide reliable experimental data. They get rejected if the characterization is incomplete, the experimental design is flawed, or the claims aren't supported by data.

This makes success more predictable than at journals where editorial impact assessment dominates decisions. You know exactly what standards to meet before submission.

Molecules averages 60-90 days from submission to first decision. That's competitive with most chemistry journals and faster than many traditional publishers.

The timeline depends heavily on reviewer availability and paper complexity. Simple synthetic papers with straightforward characterization often get reviewed faster than bioactivity studies requiring specialized expertise.

Summer months typically slow things down as academic reviewers travel or take leave. December and January also see delays around holidays.

Complex manuscripts with extensive supporting information take longer. If your paper includes multiple synthetic routes, biological assays, and computational analysis, expect the longer end of the timeline.

The editorial team generally finds reviewers within two weeks. The bottleneck is reviewer response time, not editorial processing.

Several researcher profiles fit Molecules particularly well.

Synthetic organic chemists with solid characterization data should consider this journal. If you've prepared new compounds with complete NMR, MS, and analytical data, but the synthetic methodology isn't groundbreaking enough for Organic Letters, Molecules provides a good home.

Natural product researchers find excellent fit here. The journal regularly publishes isolation studies, bioactivity screening, and synthetic approaches to natural products. The editorial board understands the field's specific requirements and timeline constraints.

Medicinal chemists with bioactivity data should look closely at Molecules. If you've synthesized compound libraries with proper biological evaluation, structure-activity relationships, and mechanistic insights, but lack the novelty for Journal of Medicinal Chemistry, this journal works well.

Industry researchers often prefer Molecules for practical reasons. The open access model ensures broad readability, the review timeline fits commercial development schedules, and the technical focus aligns with applied research goals.

Graduate students and postdocs with solid experimental work should consider submission. The journal provides good training for peer review processes without the rejection rates of top-tier venues.

How to Choose the Right Journal for Your Paper (A Practical Guide) can help you evaluate whether Molecules aligns with your specific research output.

Researchers at institutions where publication volume matters more than individual journal prestige often find Molecules attractive. The reasonable acceptance rate and straightforward requirements support productive publication strategies.