Plenty of systems work below atmospheric pressure. For example, Fridge freezers most commonly use isobutane (R600a), and when operating with the freezer at -20C, the pressure will be half an atmosphere (ie. -0.5 bar below atmospheric).
The systems are filled using a vacuum pump to ensure there is very little atmospheric air in them, and they also use a 'filter dryer', which is a chemical compound chosen to trap any remaining water and various other common contaminants.
The systems are filled using a vacuum pump to ensure there is very little atmospheric air in them, and they also use a 'filter dryer', which is a chemical compound chosen to trap any remaining water and various other common contaminants.