Brian Tomasik has a fascinating essay: Is there suffering in fundamental physics?
He admits from the start that “Any sufficiently advanced consequentialism is indistinguishable from its own parody.” And it would be easy to dismiss this as taking compassion way too far: not just caring about plants or rocks, but the possible suffering of electrons and positrons.
I think he has enough arguments to show that the idea is not entirely crazy: we do not understand the ontology of phenomenal experience well enough that we can easily rule out small systems having states, panpsychism is a view held by some rational people, it seems a priori unlikely that there is some mid-sized systems that have all the value in the universe rather than the largest or the smallest scale, we have strong biases towards our kind of system, and information physics might actually link consciousness with physics.
None of these are great arguments, but there are many of them. And the total number of atoms or particles is huge: even assigning a tiny fraction of human moral consideration to them or a tiny probability of them mattering morally will create a large expected moral value. The smallness of moral consideration or the probability needs to be far outside our normal reasoning comfort zone: if you assign a probability lower than 
I suspect most readers will regard this outside their “ultraviolett cutoff” for strange theories: just as physicists successfully invented/discovered a quantum cutoff to solve the ultraviolet catastrophe, most people have a limit where things are too silly or strange to count. Exactly how to draw it rationally (rather than just base it on conformism or surface characteristics) is a hard problem when choosing between the near infinity of odd but barely possible theories.
One useful heuristic is to check whether the opposite theory is equally likely or important: in that case they balance each other (yes, the world could be destroyed by me dropping a pen – but it could also be destroyed by not dropping it). In this case giving greater weight to suffering than neutral states breaks the symmetry: we ought to investigate this possibility since the theory that there is no moral considerability in elementary physics implies no particular value is gained from discovering this fact, while the suffering theory implies it may matter a lot if we found out (and could do something about it). The heuristic is limited but at least a start.
Another way of getting a cutoff for theories of suffering is of course to argue that there must be a lower limit of the system that can have suffering (this is after all how physics very successfully solved the classical UV catastrophe). This gets tricky when we try to apply it to insects, small brains, or other information processing systems. But in physics there might be a better argument: if suffering happens on the elementary particle level, it is going to be quantum suffering. There would be literal superpositions of suffering/non-suffering of the same system. Normal suffering is classical: either it exists or not to some experiencing system, and hence there either is or isn’t a moral obligation to do something. It is not obvious how to evaluate quantum suffering. Maybe we ought to perform a quantum-action that moves the wavefunction to a pure non-suffering state (a bit like quantum game theory: just as game theory might have ties to morality, quantum game theory might link to quantum morality), but this is constrained by the tough limits in quantum mechanics on what can be sensed and done. Quantum suffering might simply be something different from suffering, just as quantum states do not have classical counterparts. Hence our classical moral obligations do not relate to it.
But who knows how molecules feel?