P. Pulay, Analytical derivatives, forces, force constants, molecular geometries, and related response properties in electronic structure theory, WIREs: Comput. Molec. Sci, vol.4, pp.169-181, 2014.

P. Pulay, Ab initio calculation of force constants and equilibrium geometries in polyatomic molecules, Mol. Phys, vol.17, pp.197-204, 1969.

A. Warshel and M. Levitt, Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme, J. Molec. Biol, vol.103, pp.227-249, 1976.

M. J. Field, P. A. Bash, and M. Karplus, A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations, J. Comput. Chem, vol.11, pp.700-733, 1990.

H. M. Senn and W. Thiel, QM/MM Methods for Biolomolecular Systems, Angew. Chem. Int. Ed, vol.48, pp.1198-1229, 2009.

. Nobelprize and . Org, The Nobel Prize in Chemistry 2013 -Advanced Information

J. Kongsted, A. Osted, K. V. Mikkelsen, and O. Christiansen, The QM/MM approach for wavefunctions, energies and response functions within self-consistent field and coupled cluster theories, Mol. Phys, vol.100, pp.1813-1828, 2002.

A. Sinicropi, R. Basosi, and M. Olivucci, Recent applications of a QM/MM scheme at the CASPT2//CASSCF/AMBER (or CHARMM) level of theory in photochemistry and photobiology, J. Phys. Conf. Ser, vol.101, p.12001, 2008.

N. Ferré and J. G. Ángyán, Approximate electrostatic interaction operator for QM/MM calculations, Chem. Phys. Lett, vol.356, pp.331-339, 2002.

F. Melaccio, M. Olivucci, R. Lindh, and N. Ferré, Unique QM/MM potential energy surface exploration using microiterations, Int. J. Quant. Chem, vol.111, pp.3339-3346, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01415208

R. Zhang, B. Lev, J. E. Cuervo, S. Y. Noskov, and D. R. Salahub, Combining Quantum Mechanics and Molecular Mechanics. Some Recent Progresses in QM/MM Methods

J. R. Sabin and E. Brändas, Advances in Quantum Chemistry, vol.59, pp.353-400, 2010.

Y. Tu and A. Laaksonen, Combining Quantum Mechanics and Molecular Mechanics. Some Recent Progresses in QM/MM Methods

J. R. Sabin and E. Brändas, Advances in Quantum Chemistry, vol.59, pp.1-15, 2010.

V. Barone, M. Biczysko, and G. Brancato, Some Recent Progresses in QM/MM Methods; Sabin, Combining Quantum Mechanics and Molecular Mechanics, vol.59, pp.17-57, 2010.

I. Carnimeo, C. Cappelli, and V. Barone, Analytical gradients for MP2, double hybrid functionals, and TD-DFT with polarizable embedding described by fluctuating charges, J. Comput. Chem, vol.36, pp.2271-2290, 2015.

M. A. Mroginski, Encyclopedia of Biophysics

H. Springer-berlin, , pp.2149-2154, 2013.

S. Dapprich, I. Komáromi, K. Byun, K. ;. Morokuma, and F. , A new ONIOM implementation in Gaussian98. Part I. The calculation of energies, gradients, vibrational frequencies and electric field derivatives, J. Molec. Struc.: THEOCHEM, pp.1-21, 1999.

Q. Cui and M. Karplus, Molecular properties from combined QM/MM methods. I. Analytical second derivative and vibrational calculations, J. Chem. Phys, vol.112, pp.1133-1149, 2000.

Q. Cui and M. Karplus, Molecular Properties from Combined QM/MM Methods

, Chemical Shifts in Large Molecules, J. Phys. Chem. B, vol.104, pp.3721-3743, 2000.

A. Ghysels, H. L. Woodcock, J. D. Larkin, B. T. Miller, Y. Shao et al., Efficient Calculation of QM/MM Frequencies with the Mobile Block Hessian, J. Chem. Theor. Comput, vol.7, pp.496-514, 2011.

H. Nakata, T. Nagata, D. G. Fedorov, S. Yokojima, K. Kitaura et al., Analytic second derivatives of the energy in the fragment molecular orbital method, J. Chem. Phys, p.164103, 2013.

S. Sakai and S. Morita, Ab Initio Integrated Multi-Center Molecular Orbitals Method for Large Cluster Systems:â?? Total Energy and Normal Vibration, J. Phys. Chem. A, vol.109, pp.8424-8429, 2005.

A. P. Rahalkar, V. Ganesh, and S. R. Gadre, Enabling ab initio Hessian and frequency calculations of large molecules, J. Chem. Phys, p.234101, 2008.

T. Giovannini, L. Grazioli, M. Ambrosetti, and C. Cappelli, Calculation of IR Spectra with a Fully Polarizable QM/MM Approach Based on Fluctuating Charges and Fluctuating Dipoles, J. Chem. Theory Comput, vol.15, pp.5495-5507, 2019.

K. Schwinn, N. Ferré, and M. Huix-rotllant, Analytic QM/MM atomic charge derivatives avoiding the scaling of coupled perturbed equations with the MM subsystem size, J. Chem. Phys, p.41102, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02262433

P. Müller, J. Bouly, K. Hitomi, V. Balland, E. D. Getzoff et al., ATP Binding Turns Plant Cryptochrome Into an Efficient Natural Photoswitch

J. A. Pople, R. Krishnan, H. B. Schlegel, and J. S. Binkley, Derivative studies in Hartree-Fock and Møller-Plesset theories, Int. J. Quant. Chem, vol.16, pp.225-241, 1979.

A. L. Kaledin, M. Kaledin, and J. M. Bowman, All-Atom Calculation of the Normal Modes of Bacteriorhodopsin Using a Sliding Block Iterative Diagonalization Method, J. Chem. Theor. Comput, vol.2, pp.166-174, 2006.

J. A. Pople, R. Krishnan, H. B. Schlegel, and J. S. Binkley, Derivative studies in Hartree-Fock and Moller-Plesset theories, Int. J. Quant. Chem.: Quant. Chem. Symp, vol.13, pp.225-241, 1979.

R. Mcweeny, Some Recent Advances in Density Matrix Theory, Rev. Mod. Phys, vol.32, pp.335-369, 1960.

M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb et al., , 2016.

J. W. Ponder and . Tinker, Software tools for molecular design
URL : https://hal.archives-ouvertes.fr/hal-01820747

A. Baiardi, J. Bloino, and V. Barone, General Time Dependent Approach to Vibronic Spectroscopy Including Franck-Condon

, J. Chem. Theor. Comput, vol.9, pp.4097-4115, 2013.

M. Casida and M. Huix-rotllant, Progress in Time-Dependent Density-Functional Theory, Ann. Rev. Phys. Chem, vol.63, pp.287-323, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01415184

A. D. Becke, Density-functional thermochemistry. III. The role of exact exchange, J. Chem. Phys, vol.98, pp.5648-5652, 1993.

C. Lee, W. Yang, and R. G. Parr, Development of the Colle-Salvetti correlationenergy formula into a functional of the electron density, Phys. Rev. B, vol.37, pp.785-789, 1988.

S. H. Vosko, L. Wilk, and M. Nusair, Accurate spin-dependent electron liquid correlation energies for local spin density calculations: a critical analysis, Can. J. Phys, vol.58, pp.1200-1211, 1980.

A. Schäfer, H. Horn, and R. Ahlrichs, Fully optimized contracted Gaussian basis sets for atoms Li to Kr, J. Chem. Phys, vol.97, pp.2571-2577, 1992.

A. Schäfer, C. Huber, and R. Ahlrichs, Fully optimized contracted Gaussian basis sets of triple zeta valence quality for atoms Li to Kr, J. Chem. Phys, vol.100, pp.5829-5835, 1994.

K. Eichkorn, O. Treutler, H. Öhm, M. Häser, and R. Ahlrichs, Auxiliary basis sets to approximate Coulomb potentials, Chem. Phys. Lett, vol.240, pp.283-290, 1995.

K. Eichkorn, F. Weigend, O. Treutler, and R. Ahlrichs, Auxiliary basis sets for main row atoms and transition metals and their use to approximate Coulomb potentials, Theor. Chem. Acc, vol.97, pp.119-124, 1997.

D. A. Case, I. Y. Ben-shalom, S. R. Brozell, D. S. Cerutti, T. E. Cheatham et al.,

S. Lee, P. Legrand, C. Li, J. Lin, T. Liu et al., , 2018.

J. Antony, D. Medvedev, and A. Stuchebrukhov, Theoretical study of electron transfer between the photolyase catalytic cofactor FADH(-) and DNA thymine dimer, J. Am. Chem. Soc, vol.122, p.1057, 2000.

K. S. Conrad, C. C. Manahan, and B. R. Crane, Photochemistry of flavoprotein light sensors, Nat. Chem. Biol, vol.10, pp.801-809, 2014.

M. P. Kabir, Y. Orozco-gonzalez, and S. Gozem, Electronic spectra of flavin in different redox and protonation states: a computational perspective on the effect of the electrostatic environment, Phys. Chem. Chem. Phys, vol.21, pp.16526-16537, 2019.

P. Mondal, K. Schwinn, and M. Huix-rotllant, Impact of the redox state of flavin chromophores on the UVâ??vis spectra, redox and acidity constants and electron affinities, J. Photochem. Photobiol. A: Chem, p.112164, 2020.
URL : https://hal.archives-ouvertes.fr/hal-02394980

B. Klaumünzer, D. Kröner, and P. Saalfrank, TD-)DFT Calculation of Vibrational and Vibronic Spectra of Riboflavin in Solution, J. Phys. Chem. B, vol.114, pp.10826-10834, 2010.

Z. C. Holden, B. Rana, and J. M. Herbert, Analytic gradient for the QM/MM-Ewald method using charges derived from the electrostatic potential: Theory, implementation, and application to ab initio molecular dynamics simulation of the aqueous electron, J. Chem. Phys, p.144115, 2019.

A. Kalstein, S. Fernández-alberti, A. Bastida, M. A. Soler, M. H. Farag et al., Vibrational dynamics of polyatomic molecules in solution: assignment, time evolution and mixing of instantaneous normal modes, Theor. Chem. Acc, vol.128, pp.769-782, 2011.

D. R. Nutt and M. Meuwly, Theoretical Investigation of Infrared Spectra and Pocket Dynamics of Photodissociated Carbonmonoxy Myoglobin, Biophys. J, vol.85, pp.3612-3623, 2003.

C. J. Mackie, A. Candian, X. Huang, E. Maltseva, A. Petrignani et al., The anharmonic quartic force field infrared spectra of three polycyclic aromatic hydrocarbons: Naphthalene, anthracene, and tetracene, J. Chem. Phys, p.224314, 2015.