The most common and most likely answer to this crossword clue is the 9 letter word FULLERENE
I've seen this crossword clue in The Guardian
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Buddy explains!

The straight part
We know that "carbon molecule" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case carbon molecule = fullerene.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.
What does FULLERENE mean?
FULLERENE noun- Any of a class of allotropes of carbon having hollow molecules whose atoms lie at the vertices of a polyhedron having 12 pentagonal and 2 or more hexagonal faces.
- Any closed-cage compound having twenty or more carbon atoms consisting entirely of 3-coordinate carbon atoms.
- (by extension) The class of carbon allotropes consisting of tubular carbon molecules (carbon nanotubes) and spheroidal carbon molecules (traditional fullerenes).