There are provided compounds and methods for amidating the C-terminus of a polypeptide. The methods include reacting a polypeptide which includes a C-terminal thioester or C-terminal selenoester with any one of a defined set of auxiliary molecules under conditions suitable to produce a polypeptide adduct which includes the auxiliary molecule chemically bound at the C-terminal of the polypeptide. The auxiliary molecule can be a substituted or unsubstituted 2-phenyl-2-amino ethanethiol, a substituted or unsubstituted 2-phenyl-2-amino ethaneselenol, or a substituted xanthene. In the subsequent step, a portion of the auxiliary molecule is removed from the C-terminal of the polypeptide adduct and leaving the amide nitrogen under conditions suitable to form a C-terminal free amide polypeptide.