Nanoscale windows in graphene (nanowindows) have the ability to switch between open and closed states, allowing them to become selective, fast, and energy-efficient membranes for molecular separations. These special pores, or nanowindows, are not electrically neutral due to passivation of the carbon edges under ambient conditions, becoming flexible atomic frameworks with functional groups along their rims. Through computer simulations of oxygen, nitrogen, and argon permeation, here we reveal the remarkable nanowindow behavior at the atomic scale: flexible nanowindows have a thousand times higher permeability than conventional membranes and at least twice their selectivity for oxygen/nitrogen separation. Also, weakly interacting functional groups open or close the nanowindow with their thermal vibrations to selectively control permeation. This selective fast permeation of oxygen, nitrogen, and argon in very restricted nanowindows suggests alternatives for future air separation membranes.