( But ( that ( ( 's ( what ( matter ( is ( when ( ( the ( empty space ) ) ( is ( removed ( between ( ( ( the nucleus ) and ) ( ( the electrons ) ( of atoms ) ) ) ) ) ) ) ) ) ) ) ) . ) ) )
(ROOT (S (CC But) (NP (DT that)) (VP (VBZ 's) (SBAR (WHNP (WP what)) (S (NP (NN matter)) (VP (VBZ is) (SBAR (WHADVP (WRB when)) (S (NP (DT the) (JJ empty) (NN space)) (VP (VBZ is) (VP (VBN removed) (PP (IN between) (NP (NP (DT the) (NN nucleus)) (CC and) (NP (NP (DT the) (NNS electrons)) (PP (IN of) (NP (NNS atoms)))))))))))))) (. .)))
But that's what matter is when the empty space is removed between the nucleus and the electrons of atoms.
(ROOT (S (NP (DT The) (NN nucleus)) (VP (VBZ is) (VP (VBN comprised) (ADVP (RB primarily)) (PP (IN of) (NP (JJ empty) (NN space))))) (. .)))