Why did Rappaccini poison his daughter?

Rappaccini poisoned his daughter because the pursuit of scientific knowledge is more important to him than anything else, even his daughter.

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As Professor Baglioni tells Giovanni, Rappaccini

cares infinitely more for science than for mankind.

Baglioni goes on to say that Rappaccini would sacrifice anyone, even himself or someone he loved, for scientific knowledge. As Baglioni puts it,

He would sacrifice human life, his own among the rest, or whatever else...

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As Professor Baglioni tells Giovanni, Rappaccini

cares infinitely more for science than for mankind.

Baglioni goes on to say that Rappaccini would sacrifice anyone, even himself or someone he loved, for scientific knowledge. As Baglioni puts it,

He would sacrifice human life, his own among the rest, or whatever else was dearest to him, for the sake of adding so much as a grain of mustard-seed to the great heap of his accumulated knowledge.

It is this cold and obsessive thirst for knowledge that causes Rappaccini to use even his beloved daughter. The scientist researches poisons, and this leads him to poison his daughter so that she can work with, touch, and inhale his deadly poisonous plants without being harmed. However, this leaves her isolated, as her breath kills normal life. Her father, to give her a companion, arranges for Giovanni also to be poisoned so that his breath, too, becomes fatal.

In his madness, Professor Rappaccini believes he has done his daughter a favor in offering her a power that other humans lack. When she accuses him of forcing her to live in misery, he responds,

Misery, to be able to quell the mightiest with a breath? Misery, to be as terrible as thou art beautiful?

Rappaccini projects his own love of knowledge on his daughter, thinking she is as willing as he is to pay any price to advance science. He does not realize that there are limits to what is acceptable in the pursuit of knowledge and power, because, in his singlemindedness, he has completely lost his moral compass. He loves his daughter, but not enough to realize the implications of what he has done to her and that she would prefer to death to sacrificing additional people, like Giovanni, to her father's cause.

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