Chemistry commons

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The Chemistry Commons is an effort to facilitate the connections between

  • synthetic organic chemists
  • biologists seeking new reagents for biology
  • as well as medicinal chemists and computational chemists.


  • Synthetic organic chemists looking to make their chemistry available to explore.
  • Chemists use the chemistry commons to articulate and enumerate libraries of accessible compounds
  • With our assistance, libraries in 2D and 3D are prepared and made available.
  • Medicinal chemists and biologists seeking new chemistry for their biological targets use our tools to search, download, and dock these libraries
  • Compounds are prioritized for synthesis, and an agreement is made between the synthetic chemist and the biology lab testing the compounds
  • Ideally, compounds are produced, tested, and, ideally, some compounds will work.

How to get started

If you are a synthetic organic chemist, with a new reaction scheme, please use our tools to define your reaction. CC:Library preparation

If you are a biologist or medicinal chemist, seeking new compounds for your target, you can search the libraries in 2D using Smallworld CC:Smallworld and Arthor CC:Arthor or in 3D using docking or other 3D methods. CC:Docking

If you would like to participate in the chemistry commons, but are not quite sure how to get started, please reach out to chemistry4biology at gmail dot com.

Literature references

Research Groups


Naming conventions

ZINC-22 molecules have the form ZINCnprxnnnnnnnn where

  • n indicates the heavy atom count of the molecule
  • p indicates the calculated logP of the molecule
  • r indicates the research group that orginated the reaction scheme
  • x indicates the ordinal number of the reaction scheme from that research group
  • n is the ordinal for each molecule in this space.
  • numbers are in radix-62, thus [0-9][a-z][A-Z]

Synthetic organic research groups may or may not actually do the synthesis.

Notes for Chemistry Commons developers