I think something to keep in mind is that the output of knowledge work is highly sensitive to the focus and entheusiasm put in by those doing the work. Commanding people to get focused exactly when you'd like them to be focused isn't necessarily going to fly. Better to accomidate and discover (or let the employees discover) when it is that they can be most focused, and under what conditions. If they're just not "on" from say 2:30 to 4:30, but are really on at 9am and 6pm, then so be it.

That said, there is something to be said for negotiating so that employees are working at roughly the same time. I know from personal experience that it can be hard to sync with your co-workers if they're on completely opposite schedules. Though that is not the premise of this thread anyways.