There is a brief note in The New York Times explaining Why Onions Make Us Cry? It turns out that when we cut onions it releases  a chemical called lachrymatory factor (LF) which irritates our eyes. LF is by product of two molecules located in cells: sulfenic acid precursor floating around and a protein called alliinase in cytoplasm, which are released when onions are crossed and produce irritating LF. This chemical is used by plants as defense mechanisms from microbes & animals. An undergraduate student Josie Silvaroli, an undergraduate at Case Western Reserve University in Ohio helped explained this puzzle in a paper published in ACS Chemical Biology in July 2017.