Can an uncharged particle pass through a molecular bond?
The molecular bond is not a solid thing. It is merely an energetically suitable arrangement of atoms and their electrons. So another particle that happens to come close to that bond can only interact with those atomic nuclei and electrons. Whether it does interact depends.

Which particles can interact?

Considering electron-magnetic forces only:


Charged particles can interact.
Uncharged small particles can not interact.
Larger uncharged particles (e.g. other small molecules) could get polarized. This means they develop partial charges which then can interact.


How can charged particles interact with the bond?


Slow particles (with low kinetic energy) can get attracted or be repelled by the molecule, depending on the (partial) charges of the particle and molecule. If it gets attracted a chemical reaction can happen.
Fast particles (with high kinetic energy) might just pass through the molecular bond. The bond has actually much less electron density then any atom. Depending on how close it gets to an atomic nuclei, it might get deflect. Or it may even deflect the atom and break the bond. The particle could also grab or deflect an electron of the bond and thus ionize the molecule.
As a third option: there is always a slight chance of quantum tunneling.


Does this ever happen in real life?

Actually a lot: Neutrinos have no electric charge and almost no mass. As a result they can pass through matter without any consequences. They are emitted by stars and pass through earth by millions per second.

An example for charged particles would be using an electron gun to ionize molecules for mass spectrometry. The electron gun creates a beam of fast electrons, which can remove an electron from the targeted molecule upon collision (1 goes in, 2 go out).

Is there a physical size limit?

If the particle becomes larger than the molecular bond is long ... well I would not call it "passing through the bond" anymore. But the above concepts would still be the same.