( Isomers ( ( ( ( ( are ( molecules ( with ( the ( same atoms ) ) ) ) ) , ) but ) ( in ( a ( different arrangement ) ) ) ) . ) )
(ROOT (S (NP (NNS Isomers)) (VP (VP (VBP are) (NP (NP (NNS molecules)) (PP (IN with) (NP (DT the) (JJ same) (NNS atoms))))) (, ,) (CC but) (VP (PP (IN in) (NP (DT a) (JJ different) (NN arrangement))))) (. .)))
Isomers are molecules with the same atoms, but in a different arrangement.
(ROOT (S (NP (NP (NNS Alkenes)) (PP (IN with) (NP (NP (DT the) (JJ same) (NNS atoms)) (PP (CC but) (NP (JJ different) (NNS shapes)))))) (VP (VBP are) (VP (VBN called) (NP (NNS isomers)))) (. .)))