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The men with whom were having discussion did not seem very friendly.

In the sentence above, why does the adjective clause (whom were having discussion) is introduced by a preposition with... isn't it an clause is directly after a noun it describes?
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Question: is the intent of the sentence "The men who were having a discussion did not seem very friendly" or "The men, with whom we were having a discussion, did not seem very friendly"?

If the first, then with should not be added to the sentence, as it's a conjunction and there is no "other" to link the men to. And that's that.

If the second, then here goes:

It's because whom is in the objective case, thus is usually not a great way to begin a sentence or clause of any sort. Objective = being acted upon, or receiving the action of the sentence or clause. In this case the clause has the men as object, we as subject (even though the overall sentence has men as the subject); hence the pronoun must be in the objective case.

You need a conjunction to link whom with its precedent, in this case with.

Thus you would say "The men, with whom we were having the discussion, did not seem very friendly.".

You could also say "The men, whom we were having a discussion with, did not seem very friendly.".

with is required one way or the other, regardless of proximity to the referent of the clause.

You could leave out the commas; I have always had a tendency to over-comma (AmEng) myself.
 Philip's reply was promoted to an answer.