( ( ( ( ( ( ( The ( blue orbitals ) ) ( in ( the ( transition states ) ) ) ) ( are ( ( the ones ) ( forming ( the ( new ( sigma bonds ) ) ) ) ) ) ) , ) and ) ( ( the ( red orbitals ) ) ( are ( where ( ( the ( new ( double bond ) ) ) ( will ( be ( in ( the product ) ) ) ) ) ) ) ) ) . )
(ROOT (S (S (NP (NP (DT The) (JJ blue) (NNS orbitals)) (PP (IN in) (NP (DT the) (NN transition) (NNS states)))) (VP (VBP are) (NP (NP (DT the) (NNS ones)) (VP (VBG forming) (NP (DT the) (JJ new) (NN sigma) (NNS bonds)))))) (, ,) (CC and) (S (NP (DT the) (JJ red) (NNS orbitals)) (VP (VBP are) (SBAR (WHADVP (WRB where)) (S (NP (DT the) (JJ new) (JJ double) (NN bond)) (VP (MD will) (VP (VB be) (PP (IN in) (NP (DT the) (NN product))))))))) (. .)))
The blue orbitals in the transition states are the ones forming the new sigma bonds, and the red orbitals are where the new double bond will be in the product.
(ROOT (S (NP (DT A) (JJ double) (NN bond)) (VP (VBZ consists) (PP (IN of) (NP (NP (CD one) (NN sigma) (NN bond)) (CC and) (NP (CD one) (NN pi) (NN bond))))) (. .)))