How is it possible to send message in slack directly to the user, by user.id as application.
this application has scope: bot,channels:write,emoji:read,users:read,us
If I understand your question correctly, you want to send direct messages to users in the app channel instead of the standard slackbot channel.
In order to do that you need to
bot scope and a bot userMake sure to use your bot access token (not the user access token) from your Slack app.
The bot scope gives you all permissions needed to open and send DMs to users from your bot channel. No other scopes are required.
You can also use the new conversations methods, which work for all kind of channel types to do the same.
See also this question on the same topic.