The protein environment restricts the intramolecular charge transfer character of the luciferine/luciferase complex

The electronic characterization of the luciferine/luciferase complex is fundamental to tune its photophysical properties and develop more efficient devices based on this luminiscent system. Here, we apply molecular dynamics simulations, hybrid quantum mechanics/molecular mechanics (QM/MM) calculations and transition density analysis to compute the absorption and emission spectra of luciferine/luciferase and analyze the nature of the relevant electronic state and its behaviour with the intramolecular and intermolecular degrees of freedom. It is found that the torsional motion of the chromophore is hampered by the presence of the enzyme, reducing the intramolecular charge transfer nature of the absorbing and emitting state. In addition, such a reduced charge transfer character does not correlate in a strong way neither with the intramolecular motion of the chromophore nor with the chromophore/amino-acid distances. However, the presence of a polar environment around the oxygen atom of the thiazole ring of the oxyluciferin, coming from both the protein and the solvent, enhances the charge transfer character of the emitting stateWe thank the support of the Spanish Ministry of Science and Innovation through the project PID2020-117806GA-I00 funded by MCIN/AEI/10.13039/501100011033, the Comunidad de Madrid through the Attraction of Talent Program (Grant ref 2018-T1/ BMD-10261) and the Universidad Autónoma de Madrid through the Ayudas para el Fomento de la Investigación en Estudios de Master program and the predoctoral Contract Formación de Personal Investigador (FPI-UAM). The work has been performed under the Project HPC-EUROPA3 (INFRAIA2016-1-730897), with the support of the EC Research Innovation Action under the H2020 Programme and the CINECA computing center. D.A. and M.G thank funding from the European Union’s Horizon 2020 research and innovation program under the H2020-NMBP-TO-IND-2018-2020/DT-NMBP-09-2018 grant agreement No. 814492 (SIMDOME

MoBioTools: a toolkit to setup quantum mechanics/molecular mechanics calculations

We present a toolkit that allows for the preparation of QM/MM input files from a conformational ensemble of molecular geometries. The package is currently compatible with trajectory and topology files in Amber, CHARMM, GROMACS and NAMD formats, and has the possibility to generate QM/MM input files for Gaussian (09 and 16), Orca (≥4.0), NWChem and (Open)Molcas. The toolkit can be used in command line, so that no programming experience is required, although it presents some features that can also be employed as a python application programming interface. We apply the toolkit in four situations in which different electronic-structure properties of organic molecules in the presence of a solvent or a complex biological environment are computed: the reduction potential of the nucleobases in acetonitrile, an energy decomposition analysis of tyrosine interacting with water, the absorption spectrum of an azobenzene derivative integrated into a voltage-gated ion channel, and the absorption and emission spectra of the luciferine/luciferase complex. These examples show that the toolkit can be employed in a manifold of situations for both the electronic ground state and electronically excited states. It also allows for the automatic correction of the active space in the case of CASSCF calculations on an ensemble of geometries, as it is shown for the azobenzene derivative photoswitch caseSpanish Ministry of Science and Innovation; MCIN/AEI, Grant/Award Numbers: PID2020-117806GA-I00, PID2019-110091GB-I00; María de Maeztu, Grant/Award Number: CEX2018-000805-M; Comunidad de Madrid, Grant/Award Number: 2018-T1/BMD-10261; Xunta de Galicia, Grant/Award Number: GRC2019/24; the European Social Fund; Spanish Ministry of Education and Vocational Training, Grant/Award Number: FPU19/02292; Universidade de Vigo, Grant/Award Number: PREUVIGO-21; Universidad Autonoma de Madri