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2-Nitrobenzyl bromide is used in the preparation of S-2-nitrobenzyl-cysteine by reaction with L-cysteine. It is also used for the introduction of the 2-nitrobenzyl protecting group in organic synthesis. It plays an important role in the production of expectorant agent. Further, it is employed for caging unprotected cysteine-containing or thiophosphorylated peptides in aqueous solution. In addition to this, it is used in the preparation of (R)- and (S)-3-amino-3,4-dihydro-1H-quinolin-2-one.

2-Nitrobenzyl bromide reacts with L-cysteine to form S-2-nitrobenzyl-cysteine which was used for modification of ultra-low-gelling-temperature (ULGT) agarose.