I want to perform docking studies using ligands that contain stable carbenes, but the preparation or docking process changes the carbene atom types. How do I overcome this?

Most carbenes are present in highly reactive triplet or singlet intermediate states, which generally undergo reactions by forming covalent linkages. This is most likely the case with the stable carbenes as well. Most force fields do not have atom types or parameters for carbenes. Glide is intended for use with molecules that are bound by noncovalent interactions, so it is not suitable for docking carbenes.

You could try performing covalent docking studies for these species. If you know the the exact nature of the covalent link that the carbenes are involved in, you can use this information to perform a docking study using Prime Covalent Docking, which is available starting with Suite 2009.

You could also use Qsite to treat such systems, which uses a QM/MM approach wherein transition state searches can be performed.

Keywords: atom type, carbene, covalent docking

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