Nothing touches anything, and it’s not 99% empty space, it’s pretty much entirely empty space. The repulsive forces electrons feel for each other are what you feel when you touch something. The electrons on the very edge of your skin are reacting to the electrons in whatever it is you’re touching, and they never actually make contact. And electrons are themselves “point particles” with no actual size, just an area of influence.
If everything was completely smooth at the atomic scale, you’d just slide off some materials and stick to others (things with intermolecular forces, eg van der waals).
However, in the macro world, surfaces look more like stepped terrain, with hills and valleys. These can lock together between materials, forming friction. Think atomic scale velcro.
You’re way over thinking this. You’re also grossly overestimating how large an atoms is. They are so tiny and do in fact undergo bonding and electron exchange which means molecules will stay together. It’s not like you could simply move mass through the atoms of a molecule. Atoms strongly interact and there are such a large, unfathomable number of atoms in every object that the effects of atoms being mostly empty space are negligible. You need to think in terms of how the real world actually works and not how it should work based on 1 piece of information about quantum physics.
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