Chemdex: classification of atom environments in compounds

About Chemdex

Chemdex contains more than 71,000 atom environments. This is a "Request for Comment" version 1.3.1 (November 2023, compared to version 1.3 new compounds and deletions of some duplicate entries). You do not need an account to use Chemdex. The Chemdex system calculates or records several classifications (listed below) for each compound. Quick start: try the following links to view periodic trends for any of the following:

  • VN: Valence Number;
  • ON: Oxidation Number;
  • CN: Coordination Number;
  • EN: Electron Number;
  • XN: X Number;
  • LN: L Number;
  • ZN: Z Number;
  • MLXZq class (q: overall charge of the compound) and the MLXZ equivalent neutral class (ENC);
  • BN: Bond Number, or LBN: Ligand Bond Number;

There is no online documentation as yet. Use the menu items at the top to explore - or select from the below table. If you feel it would be useful to plot other pairs of classifications please let me know. You can also use the menu items to plot one property against another for one or more elements. The interface for element selection is a periodic table whose organisation is based upon the empirical data contained within Chemdex.

ON VN vs. ON
CN VN vs. CN ON vs. CN XN vs. CN
EN VN vs. EN ON vs. EN CN vs. EN
BN VN vs. BN ON vs. BN CN vs. BN LN vs. BN

Chemdex Notes

You don't need an account to browse. Please understand the compound entries are still pretty messy (necessary for debugging and programming purposes).

Chemdex contains compounds for which there is a crystal structure with coordinates on deposit and for which there is a DOI link.

If you see a pink box with a message please let me know - it indicates an error, probably in programming. Please tell me the text, the URL, what you were doing, and maybe a screenshot if you think that would help me to fix it.

Other errors: if you spot an error in the data (shouldn't be difficult) please let me know the compound and what you think is wrong. Typical errors might be incorrect attached group, incorrect attached group number, wrong name, and so on.... A good way to search for errors is to look at the outliers on the data plots. An outlier is either an interesting compound or I've made an error regarding that compound (quite likely). Note that agostic interactions are not included as primary bonding.

Chemdex should display just fine on a mobile device. It works for me on an iPhone and an iPad. Does it work on your devices? Please let me know where it does not.