Diagnose grinding sound from single rear cog
This could conceivably be a cross-chain issue. Hypothesis: when the chain is on the second cog, it extends toward the chain ring at such an angle that there is interference from the teeth of the larger, third cog.

This kind of thing can't be diagnosed remotely without detailed pictures at suitable angles showing the chain line, derailleur and cassette details and so forth.

Like user zipzit commented: get it in a stand and try to pinpoint the source of the noise. When you find it, slow down to a crawl and try to find the exact location of the metal-on-metal action. If it needs load to reproduce, have someone apply the brake to the wheel.