Running can both waken and refresh you. The one downside of training at this hour is that morning runners seem to get injured more often than afternoon runners. That's probably because they're stiff getting out of bed. To combat this problem, start your morning run by walking or running very slowly, then stop to do some brief stretching exercises before continuing. If you have an hour or more for lunch, you may be able to squeeze a workout in at this time.
Some offices have health clubs with showers and encourage workers to exercise mid-day.
Learn to manage your time. Plan your lunch in advance so you can grab a quick cup of yogurt or bowl of soup before returning to work. Noon is a good time to run during the winter when temperatures can be warmer, but bad for that same reason during the dog days of summer. Stop for a workout on your way home from work. Or go for a quick run before dinner after returning home.