Why is "phenyl" the name for the substituent variant of a benzene ring and "benzyl" refers to something slightly different (-CH2-Ph)? Also, since phenylalanine has a benzyl side-group, why isn't it called benzylalanine?

Are these inconsistencies due to historical reasons or is there some further logic that I'm missing?

The naming conventions for phenyl and benzyl originate from the historical development of organic chemistry. Phenyl refers to the substituent variant of a benzene ring, denoted as -Ph, where the benzene ring is considered as a single unit. Benzyl, on the other hand, refers to a slightly different group, denoted as -CH2-Ph, where a methyl group (-CH2-) is attached to the benzene ring.

The reason for these naming inconsistencies lies in the historical evolution of organic chemistry nomenclature. The term "phenyl" was introduced in the mid-19th century, when chemists began to study and name compounds derived from benzene. It was chosen to describe the substituent variant of benzene to keep the name distinct from benzene itself.

The term "benzyl" came later, as chemists discovered and studied organic compounds where a methyl group was attached to the phenyl group. The "benzyl" name was chosen to indicate that it is a variant of phenyl with one additional carbon (-CH2-) attached. This naming convention allows chemists to describe the structure and composition of the compound more precisely.

As for the case of phenylalanine, it is called so because it is derived from the amino acid alanine, with a phenyl group substituted for one of the hydrogen atoms in the side chain. The term "phenylalanine" is an exception to the naming convention of using "benzyl" when a methyl group is attached to a phenyl group. In this case, the name "phenylalanine" was established before the naming convention of "benzyl" was widely applied.

In summary, the inconsistencies in the naming conventions of phenyl and benzyl are mainly due to historical reasons. The term "phenyl" was introduced earlier to refer to the substituent variant of benzene, while "benzyl" was later coined to specifically describe the -CH2-Ph group. The naming of compounds like phenylalanine follows historical conventions, which sometimes deviate from strict systematic rules.