The most common and most likely answer to this crossword clue is the 9 letter word BUCKYBALL
I've seen this crossword clue in Independent
B
U
C
K
Y
B
A
L
L
Buddy explains!

The straight part
We know that "molecule" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case molecule = buckyball.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 BUCKYBALL mean?
BUCKYBALL noun- A buckminsterfullerene molecule (C60).
- (by extension) The most common types of spheroidal fullerenes, C60 and C70 usually, with additionally C72 and C76 also included at times.
- (by extension) Any spheroidal fullerene, from C20 on upwards.