boiling, then cooling, then boiling, then cooling etc. and repeating this process is an old alchemical process that is supposed to distill water down to it true essence. i have no idea if boiling water creates negative ions. however, i do know that boiling water for long periods of time before consuming it is a tradition in many philosophies.
why don't you first boil the water for 20 minutes, then energize it? that might work out great!