Chalcogenide exchange reactions are an important class of bimolecular nucleophilic substitution reactions (S_N2) involving sulfur and selenium species as nucleophile, central atom, and/or leaving group, which are fundamental throughout redox biology and metabolism. While thiol-disulfide exchange reactions have been deeply investigated, those involving selenium are less understood, especially with regards to the polarised selenenyl sulfides RSe–SR’. This functional group, which is fundamental in the biochemistry of glutathione peroxidase and thioredoxin reductase enzymes, was recently incorporated in the molecular scaffold of a TrxR1 specific probe, “RX1”. Here, we investigate the S_N2@S and S_N2@Se reactions of selenenyl sulfides in silico to provide the first comprehensive overview of their kinetic and thermodynamic trends, referencing against symmetrical disulfides and diselenides. Then, the role of S_N2@S and S_N2@Se reactions in RX1 chemistry is explored, and a mechanistic picture of its biological chemistry is provided. Additionally, we quantify the role of alternative exchange reactions in the double-exchange chemistry of RX1. This analysis rationalises the origins of RX1’s TrxR-specificity even within thiol-rich cellular environments and can support the design and applications of a range of selenenyl sulfide-based bioactive probes. Particularly, we observe that the intramolecular S_N2@Se reaction which restores RX1 ground state is an effective protective mechanism against unspecific activation by thiols, explaining its capacity to work in high-thiol concentration.