The Project

The Chemical Structures Project aims to provide a complete set of 3D molecular structures in CML format.[1] As CML format permits to include more than a simple structure, each file contains also additional informations, like molecular weight, boiling point, melting point or InChI code.[2] A CML file can also be easily converted to other file formats with Open Babel, a Free Software for chemical data file convertion.[3]

Each structure is generated with Ghemical, a free software for molecular modelling.[4] The 3D structure is modellised by a Monte Carlo simulation using the MOPAC/PM3 (v7-1.11) method.[5] Each compound is named by its common name, but the CML file contains also the IUPAC name.[6]. The formula, the mass and the exact mass are computed with Open Babel. Melting points and boiling points are values founded in the literature. If the different values given in the literature are not concordent, then a mean value is calculated. For each boiling and melting points, an error value is also calculated.

You can find further informations about this project on the Project Area of SourceForge.

Online Access

You can access the last version of this project by browsing the following links. The project is using the Jmol applet[7] for 3D visualisation. Therefore, you need to have a working java environment on your computer. The webpages are available in three languages:


Two types of archive are available:

All files are available from the download area (hosted on SourceForge).

New structure

If you want to request a new structure, simply send me an e- mail with the name and/or the 2D structure!


These files are released under the BSD license. This license permits you to modify any files, and to distribute either the original or the customized file without restriction.


  1. CML - The Chemical Markup Language
  2. InChi - The IUPAC International Chemical Identifier
  3. OpenBabel - The Open Source Chemistry Toolbox
  4. Ghemical - A Computational Chemistry Package
  5. MOPAC - A Semiempirical Quantum Chemistry Program
  6. IUPAC - International Union of Pure and Applied Chemistry
  7. Jmol - An Open Source Molecule Viewer