Fig. 3.

Computed IR spectra for the WT bacteriorhodopsin in the L state from SCC-DFTB/MM simulations (5 independent 2-ns trajectories). (A) Computed IR spectra for the QM atoms (Glu-194/204 side chains, the excess proton and 3 water molecules treated with SCC-DFTB); the spectra region of most importance here is highlighted in blue. (B and C) the continuum band in 1,800–2,000 cm⁻¹ disappears if only 1 of the Glu side chains (Glu 194 in B and Glu-204 in C) is treated with QM, which confirms that the continuum band arises because of the delocalized nature of the excess proton.