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| 1996 | Molecules was launched by Dr. Shu-Kun in collaboration with Springer Verlag as one of the first electronic journals on chemistry. |
| 1997 | MDPI took over the publishing of Molecules from Springer Verlag and started to publish it as an open access journal. Dr. Derek McPhee started working part-time as an Editorial Assistant to the then Editor-in-Chief of Molecules, Dr. Esteban Pombo-Villar. |
| 1999 | Dr. Shu-Kun Lin took over as Editor-in-Chief of Molecules. |
| 2005 | Dr. Derek McPhee accepted the role of Editor-in-Chief of Molecules after acting as Managing Director of the journal since 1999, while the former Editor-in-Chief Dr. Shu-Kun Lin held title of Publisher and Director of the Molecules Editorial Office. Molecules celebrated its tenth anniversary. |
| 2005-2006 | Papers were published in both non-Open Access (non-OA) and Open Access (OA) form. |
| 2007 | Molecules publishes exclusively in Open Access form. |
| 2008 | Molecules adds the Digital Object Identifier (DOI) numbers to each paper using the CrossRef system. The Open Access logo is added and copyright is under the Creative Commons (CC) license v. 3.0. |
| 2012 | The first Best Paper Award was announced. |
| 2013 | The Section Metabolites was established. Molecules received an impact factor of 2.428 for the year 2012; the 5-year impact factor is 2.679. |
| 2014 | Molecules published its 6,000 paper. |
| 2015 | Four new sections, Green Chemistry, Photochemistry, Bioorganic Chemistry and Organometallic Chemistry were established. Molecules published its 8,000 paper. |
| 2016 | Molecules published its 10,000 paper. The first Tu Youyou Award was announced. |
| 2017 | Molecules expanded the scope. Five new sections, Inorganic Chemistry, Physical Chemistry, Analytical Chemistry, Nanochemistry and Chemical Biology were established. The 1st Molecules Medicinal Chemistry Symposium, organized by Molecules, was held. |
| 2018 | Two sections, Metabolites and Molecular Diversity were closed. At the same time, two new sections, Materials Chemistry and Electrochemistry were established. Molecules received its highest impact factor of 3.098 for the year 2017; the 5-year impact factor is 3.268. |
Editors-in-Chief
| 1996-1999 | Founding Editor-in-Chief Dr. Shu-Kun Lin |
| 1996-2005 | Editor-in-Chief Dr. Shu-Kun Lin |
| 2005- | Editor-in-Chief Dr. Derek J. McPhee |
