How do bonds form without violating the second law of thermodynamics It might be obvious that entropy related to reactions always increases and I understand (somewhat) why this happens. My question is why if you have two hydrogen atoms in a vacuum without being bonded to a molecule they would form a bond. Does that not show a movement from chaos to order and thus a decrease in entropy?
Note that 2 isolated hydrogen atoms will not form a stable hydrogen molecule, unless they are able to dissipate the energy, released by the bond formation. It can be done e.g.  passing mechanical energy to neighbour molecules, or emitting a photon.

In a macro scale, a system can decrease its entropy, if its Gibbs energy decreases, as it means the dissipated heat causes the bigger entropy increase of the surrounding, than is the entropy decrease of the system, so the total entropy increases.

$$\Delta G = \Delta H - T \cdot \Delta S$$

If $\Delta G_\mathrm{sys} \lt 0$ then $\Delta S_\mathrm{tot}=\Delta S_\mathrm{sys} + \Delta S_\mathrm{surr} \gt 0 $

as $\Delta S_\mathrm{sys} + \Delta S_\mathrm{surr}=\Delta S_\mathrm{sys} - \frac{(\Delta G_\mathrm{sys} + T \cdot \Delta S_\mathrm{sys})}{T}=-\frac {\Delta G_\mathrm{sys}}{T}$