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We suggest closing all transactions and running a VACUUM before creating an index to avoid the calculation of the index data on rows that are being changed in the current transaction. E.g. if a column was added in the current transaction, the index creation time can be almost double of the normal time.
The same logic applies to updating a large number of molecules in an indexed table and then search on the table without closing the transaction and clearing up modification with VACUUM. If possible, update operations and column additions are advised to be performed before adding the chemical index.

Be aware that an ALTERed, not VACUUMed table can contain NULL values in the background and may force the index creation to stop.

How to follow the CREATE INDEX process

Available from version 5.0.