Why does chopping an onion make you cry?

Unstable chemicals.

Onions produce the chemical irritant known as syn-propanethial-S-oxide. It stimulates the eyes' lachrymal glands so they release tears. Scientists used to blame the enzyme allinase for the instability of substances in a cut onion. Recent studies from Japan, however, proved that lachrymatory-factor synthase, (a previously undiscovered enzyme) is the culprit (Imani et al, 2002).
The process goes as follows:

1. Lachrymatory-factor synthase is released into the air when we cut an onion.
2. The synthase enzyme converts the sulfoxides (amino acids) of the onion into sulfenic acid.
3. The unstable sulfenic acid rearranges itself into syn-ropanethial-S-oxide.
4. Syn-propanethial-S-oxide gets into the air and comes in contact with our eyes. The lachrymal glands become irritated and produces the tears!