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The section you have indicated may of course be different in my book, but I think there is lots of evidence there to answer the question you have asked. When Charlie goes to see Alice in his old classroom, Alice and he have an argument when Alice says to Charlie that becoming more intelligent has changed him from the way that he was before. Note the following quote:
"There was something in you before. I don't know... a warmth, an openness, a kindness that made everyone like you and like to have you around. Now, with all your intelligence and knowledge, there are differences that--"
Charlie becoming more intelligent has therefore changed him from the warm, sensitive person he was into somebody different. Likewise, his intelligence has had its effect on those around him. Alice goes on to say:
"But these days I can't talk to you. All I can do is listen and nod my head and pretend I understand all about cultural variants, and neo-Boulean mathematics, and post-symbolic logic, and I feel more and more stupid, and when you leave the apartment, I have to stare in the mirror and scream at myself: 'No, you're not growing duller every day! You're not losing our intelligence! You're not getting senile and dull-witted.'"
Thus Charlie's massive intelligence now makes Alice feel inadequate. The experiment that Charlie has had performed on him has apparently changed him irrevocably, and this in turn changes his relationships with those around him. It is these two essential facts that makes Alice reluctant to pursue a relationship with her former student.
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