The proton transfer (PT) mechanism involved in the bioluminescence process were obtained by p𝐾 𝑎 calculations using the PDLD method. The p𝐾 𝑎 calculations for specific PT donor-acceptor pairs should be considered together, which means in most of the calculations, p𝐾 𝑎 of the residue was calculated while the emitter was in the neutral form.