QM/MM setup

The QM/MM calculations have been carried out using a QM/MM coupling scheme (Ferré and Ángyán, 2002) between Gaussian09 (G09 D.01) (Frisch et al., 2010) and Tinker (Ponder, 2004). In particular, the interaction between the QM charge density (electrons and nuclei) and the external electrostatic potential of the MM part was computed by the electrostatic potential fitted (ESPF) method (Ferré and Ángyán, 2002). The microiterations technique (Melaccio et al., 2011) was used to converge the MM subsystem geometry for every QM minimization step. The QM part is composed of the OxyLH⁻, either in the keto or in the enol form, the AMPH and the water molecule n°559 (hereafter named Wat1), placed between the oxyluciferin and AMPH. The rest of the system, that is the protein and the water molecules, are included in the MM part.

QM/MM calculations were used for searching of the transition states (TS) in the protein, defining energetic profiles bridging the TS to the keto and enol forms, and calculating the electronic transitions between the first singlet excited state (S1) and the ground state (GS). For TS and energetic profiles search, unrestricted with broken-symmetry and restricted DFT and TD-DFT calculations were performed using the M06-2X functional (Zhao and Truhlar, 2008) which includes a dispersive term and provides accurate results when studying chemical reactions (Chéron et al., 2012). Unrestricted and restricted calculations gave similar results in terms of energy and geometries, of about 0.12 eV for the transition state (TS), and about 0.15 eV for energetics profiles. Therefore restricted results are presented in this publication. TD-DFT calculations were performed using 3 roots. The emission energy (T_e) between the first singlet excited state (S1) and the ground state (GS), from geometries obtained in the S1 state, were computed using both the M06-2X and the B3LYP (Stephens et al., 1994) functionals. The B3LYP functional is known to give emission energy values close to experiment for fireflies (Berraud-Pache and Navizet, 2016). Finally, the basis set used is the 6-311G(2d,p) as used in previous publications (Laurent et al., 2015; Berraud-Pache and Navizet, 2016).