I suspect the professor actually had a family before. And by a family, i mean his three little girls. Three, because why would a grown man adopt three kids if it wasn't for a specific reason? I believe the professor had three little girls, whose death he tried to block out by recreating them. Since he didn't try to recreate the mom, i'd say she's not dead but had abandoned her family, leaving the professor to raise his three original little girls all by himself.

But, see, the little girls weren't perfect. They had problems, they had defects. They may have been greedy, or immature, or just plain disobedient. One could suppose either their imperfection caused an accident, an accident the professor would forever try to avoid once again by creating the three perfect little girls. Overwhelmed by grief, made delusional, the professor was a genius chemist, the elite of society, however imperfection surrounded him, with his pathetic failure of a marriage, a rabid monkey always at his side and the fatal accident that took his little girls away from him. He'd never speak about them again, and would choose the most random names for his newer, perfect children ('I'll call you Blossom, Bubbles and uh...Buttercup!') The only way he could ever be truly happy would be to make sure the imperfection of the world that ruined his life would never be renewed by creating perfection out of his own hands.

However, the creation of the compound itself was an accident. The chemical X that intervened was not part of the plan. And yet Professor X realized the perfection he seeked, but failed to achieve through the creation of his three little girls, didn't bring him the kind of happiness he actually got with the powerpuff girls. The moral of the powerpuff girls is happiness exists beyond perfection.