Molecules Formatting Requirements: Complete Author Guide

Molecules follows MDPI's standardized abstract format across all its journals.

• Word limit: 200 words maximum
• Structure: Single unstructured paragraph
• Citations: Not permitted in the abstract
• Abbreviations: Define at first use in the abstract
• Mathematical formulas: Not permitted in the abstract
• Keywords: 3 to 10 keywords required, listed immediately below the abstract

The 200-word abstract is a hard limit in the submission system. It won't reject you outright, but the editorial assistant will flag abstracts over 200 words during the initial check and ask you to shorten them. This adds a round-trip to your timeline.

Molecules covers organic chemistry, medicinal chemistry, natural products, food chemistry, and materials chemistry. Because the readership is broad, your abstract needs to be accessible to chemists outside your specific niche. Don't assume the reader knows your model compound or your assay by name. State what you did and what you found in concrete terms.

MDPI journals display the abstract prominently on the article page, and it's the primary text that appears in Google Scholar results. Spending an extra 30 minutes on a sharp abstract has a real impact on readership.

Molecules follows the standard MDPI figure guidelines.

Figure specifications:

Table formatting:

• Tables must be editable (not images)
• Created using Word's table function or LaTeX table environments
• Number sequentially (Table 1, Table 2, etc.)
• Title goes above the table
• Footnotes below the table, using superscript lowercase letters (a, b, c)
• No vertical lines; horizontal lines at top, bottom, and below header only

One area where Molecules stands out from most publishers: there's no charge for color figures. This is standard across MDPI journals, and it means you don't need to design figures that work in both color and grayscale. Use color strategically for clarity, not just decoration.

Chemical structures should be drawn using ChemDraw, MarvinSketch, or equivalent software. MDPI doesn't specify a particular style sheet, but consistent bond lengths and font sizes across all structures in a manuscript are expected. Inconsistent chemical drawings are one of the most common revision requests.

Schemes (reaction schemes) are numbered separately from figures. Use Scheme 1, Scheme 2, etc. This is important because the MDPI template has a separate numbering sequence for schemes, and misnumbering causes production delays.

Molecules uses the MDPI reference style, which has one major difference from most other publishers: full journal names instead of abbreviations.

In-text citations: Numbers in square brackets, e.g., [1], [2,3], [4-7]. Numbered in order of first appearance.

Reference list format:

1. Author, A.B.; Author, C.D. Title of Article. Full Journal Name Year, Volume, Page Range.

Key formatting details:

• Author names: Surname, followed by initials with periods (e.g., "Smith, J.K.")
• Semicolons between authors
• Use the full journal name, not the abbreviation (e.g., "Journal of the American Chemical Society" not "J. Am. Chem. Soc.")
• Volume in bold, issue number in parentheses
• DOIs are mandatory for all references that have them
• For references with more than 6 authors, list all authors (don't truncate with "et al." in the reference list)

The full journal name requirement is the single most common formatting error in Molecules submissions. Authors who've published at Elsevier, Wiley, ACS, or RSC journals are used to ISO 4 abbreviations. MDPI wants the full name. If you use a reference manager, set it to the MDPI output style, which handles this automatically. Zotero, Mendeley, and EndNote all have MDPI styles available.

There's no formal reference cap, but Research Articles in Molecules typically cite 30 to 60 papers. Reviews can go well above 100.

MDPI handles supplementary material differently from most traditional publishers.

What goes in supplementary material:

• Additional experimental data (spectra, chromatograms, additional assay results)
• Extended tables that would break the flow of the main text
• Computational data (coordinates, input files)
• Video content
• Datasets

Formatting requirements:

• Submit as a single PDF file when possible, with internal numbering (Figure S1, Table S1, etc.)
• If Excel files or datasets are needed, they can be submitted as separate files
• Each supplementary item must be cited in the main text
• Supplementary files are peer-reviewed alongside the main manuscript

MDPI publishes all supplementary material as open-access alongside the article on the journal website. There are no access barriers, which is worth knowing if your supplementary material contains data you want freely accessible.

A note about NMR spectra: Molecules frequently publishes synthetic chemistry work, and reviewers routinely ask for NMR spectra in the supplementary material for all new compounds. If you're reporting new compounds, include 1H NMR, 13C NMR, and HRMS data in the supplementary file from the start. Adding them later costs you a revision cycle.

These are the details specific to Molecules that aren't obvious from a quick read of the author guidelines:

MDPI uses its own in-house XML workflow. Unlike Elsevier or Springer, MDPI doesn't rely on traditional typesetting. They convert your manuscript to XML directly, which means any formatting that doesn't follow the template structure gets lost or corrupted during conversion. This is why the template is non-negotiable, not just preferred.

Graphical abstract is optional but displayed prominently. If you provide a graphical abstract, it appears as the thumbnail image on the journal website and in social media shares. The recommended size is 560 pixels wide by 400 pixels tall. If you don't provide one, the system uses the first figure of your paper, which may not be your best visual representation.

Author affiliations use superscript numbers. MDPI uses numbered superscripts (not symbols or letters) to link authors to affiliations. The template handles this, but if you're formatting manually, get the order right. The corresponding author is marked with an asterisk, and the ORCID iD for each author is included directly in the author block.

Molecules has an open peer review option. Authors can choose to have their reviewer reports published alongside the paper. This doesn't affect formatting, but it does affect how you write your cover letter and response to reviewers, since those might become public.

Data availability statement is mandatory. Every Molecules paper must include a Data Availability Statement at the end of the manuscript (before the references). Choose from standard MDPI templates: data available in the article, data available on request, no new data created, or data available in a public repository.

Funding and acknowledgments are formatted sections. The MDPI template includes dedicated sections for Funding and Acknowledgments with specific formatting. Don't merge these into a single paragraph at the end of the paper. They need to be separate, labeled sections.

Based on common revision requests at Molecules:

1. Full journal names in references. The number one formatting error across all MDPI journals. If you use abbreviated names, every single reference will be flagged.

1. Missing ORCID iDs. MDPI strongly encourages ORCID for all authors and requires it for the corresponding author. The template includes ORCID fields in the author block.

1. Scheme vs Figure numbering. Reaction schemes must be numbered separately from figures. Labeling a scheme as "Figure 3" confuses the production system.

1. Section numbering conflicts. If you manually number sections and also use the template's auto-numbering, you'll get double numbers (e.g., "3. 3. Results").

1. Supplementary material not cited in text. Every supplementary figure and table must be referenced at least once in the main text. Orphaned supplementary items get flagged during production.

In our pre-submission review work with manuscripts targeting Molecules, four patterns generate the most consistent desk-rejection outcomes.

Mandatory MDPI template not used for submission. Molecules requires all submissions to be formatted using the official MDPI Word or LaTeX template. Manuscripts submitted in a non-MDPI template or in plain manuscript format are returned for reformatting before entering peer review. The MDPI LaTeX template uses the mdpi document class, and the Word template includes pre-formatted heading styles, figure caption styles, and reference formatting. Editors verify template compliance at the submission stage.

Abstract exceeds 200 words or contains citations, abbreviations, or equations. MDPI guidelines for Molecules state that the abstract must be no more than 200 words, unstructured, and must not contain literature citations, undefined abbreviations, or mathematical formulas. This limit is strictly enforced. Abstracts that exceed 200 words or include any citation are flagged during submission system processing. The abstract must stand alone as a complete summary covering objective, methods, key results, and conclusions.

Full journal names not used in the reference list. Molecules follows the MDPI reference style, which uses full journal names rather than standard abbreviations. This is the opposite of ACS, RSC, and Elsevier reference styles. Authors submitting from chemistry or materials science backgrounds often use abbreviated journal titles from other reference managers. The MDPI reference format requires "Journal of the American Chemical Society" not "J. Am. Chem. Soc."

Supplementary Materials not uploaded as separate files and not described in the manuscript. MDPI requires that all Supplementary Materials be uploaded as separate files during submission and referenced by file name within the manuscript text (e.g., "see Supplementary Material, Figure S1"). Manuscripts where supplementary figures are embedded in the main document or referenced without a corresponding file upload are returned for correction.

A Molecules formatting and readiness check evaluates manuscript structure, MDPI template compliance, abstract length, and reference format against these desk-rejection patterns before you submit.