However, although glycogen levels (the body's enegry stores) are likely to be higher in the afternoon as compared with early morning after an overnight fast, this is not relevant to high intensity efforts of very short duration where glycogen stores are unlikely to be depleted. Certainly I well remember taking 40 minutes for my standard course in my favourite forest at 6am one day and taking 36 minutes the following day at 12 noon for the same effort.
Most of us are governed by work routine and if we plan our training linked to work we should aim, if possible, to train at lunch time or after work. However, if this is not possible it is clearly better to run early than not at all. One of the benefits of early runs is that you have got your run in and any unexpected events which may prevent you from running through the day do not disrupt your training. I also believe that if you are a distance runner, the early runs on low glycogen prepare your body for that situation in a marathon or half marathon.
But the bottom line is that the higher the quality of your training, the better your performances are likely to be. Hence, try to run at mid-day or evening when you are at your peak.