The force between the box and the molecule will be tiny, not 10000N, although it will be reciprocal so Newton's third law will be obeyed.
You have made the example rather self-contradictory, since you have said that the box is falling as a result of gravity, yet we should ignore gravity as far as the molecule is concerned. However, for the sake of illustrating the principles involved, let us assume that gravity does not act on the molecule...
To make the scenario less ambiguous again, let us suppose the box is neutrally charged and composed of an inert substance that does not interact chemically with the O2 molecule, and that the molecule is motionless relative to the cylinder.
Given that, the approaching box will impart an electromagnetic force that will accelerate the molecule. The force will be electromagnetic- some type of Van Der Waals force, the exact form of which will depend on the shape of the surface of the box in the local area that comes closest to contact with the molecule.
The effect will be to accelerate the molecule to keep it at some equilibrium distance away from the box as the box falls. On average, therefore, the force exerted by the box on the molecule will be mg, where m is the mass of the molecule.
The principle would be clearer if the box were falling with a weightless string attached that went over a frictionless pulley and along a frictionless horizontal surface upon which the string lassoed the O2 molecule. As the box fell, it would drag the molecule along the horizontal surface. The molecule would move in pace with the box, accelerating at 1g.