Specifically, caffeine is methylated theobromine (if the chemical structure above is accurate); one of the hydrogen atoms in the theobromine molecule is replaced by a methyl group (the H3C, qhich is a pretty common "molecule acting as atom" in organic chemistry).
There's a lot of this sort of thing in organic chemistry, and methylating a molecule can change its effects somewhat (methanol versus ethanol, for instance); more commonly, the two molecules act almost but not *precisely* the same (in a less innocuous context than theobromine and caffeine, much the same goes on with amphetamine and methamphetamine--and with a *lot* of different opioid pharmaceuticals).
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There's a lot of this sort of thing in organic chemistry, and methylating a molecule can change its effects somewhat (methanol versus ethanol, for instance); more commonly, the two molecules act almost but not *precisely* the same (in a less innocuous context than theobromine and caffeine, much the same goes on with amphetamine and methamphetamine--and with a *lot* of different opioid pharmaceuticals).