I worked this one out. you have to set a combination of things to achieve it.
1. create the department eg support
2, create a user group and give the rights you want
3, create the user and make part of both the support department and user group then set the user as the department head
4, add an email and assign it to the user
5, turn off all admin email alerts
6, turn on department heads email alerts
7, add new help topic ( eg Support - IT )setting the department to support.
I think that's it. now when a user selects the new help topic on the create new ticket form an email will only be sent to the head of the selected department