As I would tell something to a specific user, can I send him a message directly to not pollute the comment thread?
As you will see at Any way to send a personal message to another user? it is by design that there is no feature on Stack Exchange to facilitate private messaging between users.
While not private, you will be free to discuss in there without polluting the comment thread. You could link to that new chat room in the comments so the user is aware of it.