( it ( ( is ( ( a molecule ) ( ( in which ) ( ( a ( hydrogen atom ) ) ( is ( replaced ( by ( a ( chlorine atom ) ) ) ) ) ) ) ) ) . ) )
(ROOT (S (NP (PRP it)) (VP (VBZ is) (NP (NP (DT a) (NN molecule)) (SBAR (WHPP (IN in) (WHNP (WDT which))) (S (NP (DT a) (NN hydrogen) (NN atom)) (VP (VBZ is) (VP (VBN replaced) (PP (IN by) (NP (DT a) (NN chlorine) (NN atom))))))))) (. .)))
it is a molecule in which a hydrogen atom is replaced by a chlorine atom.
(ROOT (S (ADVP (RB Replace)) (NP (NP (DT another)) (PP (IN in) (NP (DT a) (NN molecule)))) (VP (VBZ happens) (PP (TO to) (NP (NNS atoms))) (PP (IN during) (NP (DT a) (NN substitution) (NN reaction)))) (. .)))
Replace another in a molecule happens to atoms during a substitution reaction.