( This ( ( ( is simply ) ( sugar ( with ( ( a ( flourine atom ) ) ( replacing ( ( a ( carbon atom ) ) ( in ( the molecule ) ) ) ) ) ) ) ) . ) )
(ROOT (S (NP (DT This)) (VP (VBZ is) (ADVP (RB simply)) (NP (NP (NN sugar)) (PP (IN with) (NP (NP (DT a) (JJ flourine) (NN atom)) (VP (VBG replacing) (NP (NP (DT a) (NN carbon) (NN atom)) (PP (IN in) (NP (DT the) (NN molecule))))))))) (. .)))
This is simply sugar with a flourine atom replacing a carbon atom in the molecule.
(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.