For one, it is unlikely to cut molecules with a knife, may be superlong organic ones. I've read an article back how certain long molecules are being broke down into less useful stuff for consumption in the finely processed food. Although, I take that with a grain of salt.
Second, if you are cutting pure material, as in from the periodic table, then you are breaking bonds between atoms, e.g. cutting aluminum sheet.
Splitting atoms releases enormous amounts of energy, and nuclear(not thermonuclear), or fission bomb is just that, atoms being split.