This is probably due to limitations in the CSD search engine. The most common types of slow searches are:
- Substructure searches for groups that contain symmetry (e.g. t-butyl); these can take a very long time indeed, especially if 3D parameters are being calculated.
- Substructure searches for groups that contain only the most common elements (C,N,O) and are connected by single or Any bond types.
- Substructure searches for large (>12-membered) rings, especially if they are carbocyclic.
- Searches for nonbonded interactions especially for patterns involving more than one interaction.
- Some text searches.