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1. Not a word she didn't say to me.

2. Not that I only mind your behavior, I just hate you.

3. They were here not five minutes ago.

4. The tug crossed our stern not fifty yards away.

5. "Did he have any enemies?" - Not a one. Not a damn one!

6. Not every applicant had a degree.


I think in all the sentences above, "not" is negating the bold parts.

Except in sentence 2, "not" seems to be negating phrases in the other sentences.

Am I right?

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fire11. Not a word she didn't say to me.

Not a word did she say to me. (literary)

fire12. Not that I only mind your behavior, I just hate you.

It's not just that I mind your behavior. I hate you.

fire13. They were here not five minutes ago.

Good.

fire14. The tug crossed our stern not fifty yards away.

Good.

fire15. "Did he have any enemies?" - Not a one. Not a damn one!

Good.

fire16. Not every applicant had a degree.

Good.

fire1I think in all the sentences above, "not" is negating the bold parts.

I can only comment on the ones that are natural English, to wit, 3, 4, 5 and 6. I would say you are right except for 6, where it negates "every".

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fire1 Can "not" negate phrases and clauses?

Yes. In addition to marking verbal negation, "not" can modify a considerable range of non-verbal elements.