Fixed-charge method, polarizability calculations

Several approaches for calculating excited states in protein environments were proposed to improve the ordinary QM/MM description. The effect of polarization was included as a classical force field [27], and the excitation energy calculated for bacteriorhodopsin (bR) was 0.34 eV less than that from a fixed-charge non-polarizable QM/MM method [27]. Later, a triple-layer QM1/QM2/MM approach was proposed, and DFT(PBEO) calculations were performed for the QM2 layer, which consisted of the amino acids 4 A from the retinal PSB [28]. The calculated excitation energy of bR was only 0.08 eV smaller than that obtained using the ordinary QM/MM method [28]. In another study, an empirical polarization model combined with the QM/MM calculation produced a red shift of 0.14-0.17 eV [29]. However, these pioneering studies neglected the CT effects between the retinal and the protein environments. 

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