A reasonable basis for the puzzling variation of tryptophan (Trp) fluorescence quantum yields in proteins arises naturally through quantum mechanics-molecular dynamics simulations in which the energy of the lowest Trp ring-to-amide backbone charge transfer (CT) state is monitored during dynamics trajectories for 16 Trps in 13 proteins. The energy, fluctuations, and relaxation of the high lying CT state are highly sensitive to protein environment (local electric field) and rotamer conformation, leading to large variations in L-1(a) fluorescence yield and lifetime. (C) 2003 Elsevier Science B.V. All rights reserved.