There are molecules in the onion juice called lacrymators which are volatile and evaporate on cutting the onion open. These waft up to our eyes and cause our we eyes to water up.
When you cut an onion, it releases a chemical called propanethiol S-oxide. This is a compound containing (among others) sulfur atoms. It is released as a gas which wafts towards your eyes, and when it gets there is reacts with the water in your eyes to make tiny amounts of sulfuric acid, which irritates your eyes. As a defense mechanism, your eyes start to water, to wash out the irritating chemical! Now if you could figure out a way to use that information to come up with a way to stop the crying, I would be really grateful.
These sorts of compounds (which make you cry) are called lachrymators, from the latin lacrima, meaning tear (lacrimare = to cry).
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