O. Shimomura and . Bioluminescence, Chemical Principles and Methods, 2012.

P. J. Herring, Bioluminescence in Action, 1978.

M. Zimmer, Green Fluorescent Protein (GFP): Applications, Structure, and Related Photophysical Behavior, Chem. Rev, vol.102, pp.759-782, 2002.

R. Y. Tsien, The Green Fluorescent Protein, Annu. Rev. Biochem, vol.67, issue.1, pp.509-544, 1998.

S. J. Remington, Green Fluorescent Protein: A Perspective, Protein Sci, vol.2011, issue.9, pp.1509-1519

V. Baubet, H. Le-mouellic, A. K. Campbell, E. Lucas-meunier, P. Fossier et al., Chimeric Green Fluorescent Protein-Aequorin as Bioluminescent Ca2+ Reporters at the Single-Cell Level, Proc. Natl. Acad. Sci. U. S. A, issue.13, pp.7260-7265, 2000.
URL : https://hal.archives-ouvertes.fr/hal-00171705

H. Fraga, I. Allue, K. Bowers, P. Cobbold, T. L. Southworth et al., A Historical Perspective and Recent Developments, Photochem. Photobiol. Sci, vol.7, issue.2, p.146, 2008.

Z. M. Kaskova, A. S. Tsarkova, and I. V. Yampolsky, Lights: Luciferins, Luciferases, Their Mechanisms of Action and Applications in Chemical Analysis, Biology and Medicine. Chem. Soc. Rev, vol.45, issue.21, pp.6048-6077, 1001.

M. Griffiths, The Role of ATP Bioluminescence in the Food Industry: New Light on Old Problems, Food Technol, vol.50, pp.62-73, 1996.

R. Shinde, J. Perkins, and C. H. Contag, Luciferin Derivatives for Enhanced in Vitro and in Vivo Bioluminescence Assays, Biochemistry, vol.45, pp.11103-11112, 2006.

L. F. Greer and A. A. Szalay, Imaging of Light Emission from the Expression of Luciferases in Living Cells and Organisms: A Review, Luminescence, vol.17, issue.1, pp.43-74, 2002.

L. J. Kricka, Application of Bioluminescence and Chemiluminescence in Biomedical Sciences, Methods Enzymol, vol.305, pp.333-345, 2000.

H. Ohkuma, K. Abe, Y. Kosaka, and M. Maeda, Detection of Luciferase Having Two Kinds of Luminescent Colour Based on Optical Filter Procedure: Application to an Enzyme Immunoassay, Luminescence, vol.15, issue.1, pp.21-27, 2000.

Q. Shao, T. Jiang, G. Ren, Z. Cheng, and B. Xing, Photoactivable Bioluminescent Probes for Imaging Luciferase Activity, Chem. Commun, issue.27, p.4028, 2009.

T. C. Doyle, S. M. Burns, and C. H. Contag, In Vivo Bioluminescence Imaging for Integrated Studies of Infection. Cell. Microbiol, vol.6, issue.4, pp.303-317, 2004.

F. Fan and K. V. Wood, Bioluminescent Assays for High-Throughput Screening, Assay Drug Dev. Technol, vol.5, issue.1, pp.127-136, 2007.

E. H. White, E. Rapaport, H. H. Seliger, and T. A. Hopkins, The Chemi-and Bioluminescence of Firefly Luciferin: An Efficient Chemical Production of Electronically Excited States, Bioorg. Chem, pp.92-122, 1971.

M. F. Deluca and . Luciferase, Adv. Enzymol. Relat. Areas Mol. Biol, vol.44, pp.37-68, 1976.

I. Navizet, Y. Liu, N. Ferré, D. Roca-sanjuán, and R. Lindh, The Chemistry of Bioluminescence: An Analysis of Chemical Functionalities, ChemPhysChem, vol.12, issue.17, pp.3064-3076, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00749782

Y. Ando, K. Niwa, N. Yamada, T. Enomoto, T. Irie et al., Firefly Bioluminescence Quantum Yield and Colour Change by pH-Sensitive Green Emission, Nat. Photonics, vol.2, issue.1, pp.44-47, 2008.

Y. Wang, H. Kubota, N. Yamada, T. Irie, and H. Akiyama, Quantum Yields and Quantitative Spectra of Firefly Bioluminescence with Various Bivalent Metal Ions, Photochem. Photobiol, vol.87, issue.4, pp.846-852, 2011.

T. Mochizuki, Y. Wang, M. Hiyama, and H. Akiyama, Robust Red-Emission Spectra and Yields in Firefly Bioluminescence against Temperature Changes, Appl. Phys. Lett, vol.104, issue.21, p.213704, 2014.

Y. Wang, H. Akiyama, K. Terakado, and T. Nakatsu, Impact of Site-Directed Mutant Luciferase on Quantitative Green and Orange/red Emission Intensities in Firefly Bioluminescence, Sci. Rep, 2013.

D. M. Mofford, G. R. Reddy, and S. C. Miller, Aminoluciferins Extend Firefly Luciferase Bioluminescence into the Near-Infrared and Can Be Preferred Substrates over D -Luciferin, J. Am. Chem. Soc, vol.136, issue.38, pp.13277-13282, 2014.

G. R. Reddy, W. C. Thompson, and S. C. Miller, Robust Light Emission from Cyclic Alkylaminoluciferin Substrates for Firefly Luciferase, J. Am. Chem. Soc, issue.39, pp.13586-13587, 2010.

S. Hosseinkhani, Molecular Enigma of Multicolor Bioluminescence of Firefly Luciferase, Cell. Mol. Life Sci, vol.2011, issue.7, pp.1167-1182

T. Hirano, Y. Hasumi, K. Ohtsuka, S. Maki, H. Niwa et al., Spectroscopic Studies of the Light-Color Modulation Mechanism of Firefly (Beetle) Bioluminescence, J. Am. Chem. Soc, vol.131, issue.6, pp.2385-2396, 2009.

I. Navizet, Y. Liu, N. Ferre?, H. Xiao, W. Fang et al., Color-Tuning Mechanism of Firefly Investigated by Multi-Configurational Perturbation Method, J. Am. Chem. Soc, vol.132, issue.2, pp.706-712, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00749370

P. Naumov and M. Kochunnoonny, Spectral?Structural Effects of the Keto?Enol?Enolate and Phenol?Phenolate Equilibria of Oxyluciferin, J. Am. Chem. Soc, issue.33, pp.11566-11579, 2010.

O. V. Maltsev, N. K. Nath, P. Naumov, and L. Hintermann, Why Is Firefly Oxyluciferin a Notoriously Labile Substance? Angew. Chemie Int, vol.53, pp.847-850, 2014.

P. Naumov, Y. Ozawa, K. Ohkubo, and S. Fukuzumi, Structure and Spectroscopy of Oxyluciferin, the Light Emitter of the Firefly Bioluminescence, J. Am. Chem. Soc, vol.131, issue.32, pp.11590-11605, 2009.

B. R. Branchini, H. Martha, R. A. Murtiashaw, N. C. Magyar, M. C. Portier et al., Yellow-Green and Red Firefly Bioluminescence from 5,5-Dimethyloxyluciferin, J. Am. Chem. Soc, vol.124, pp.2112-2113, 2002.

M. Rebarz, B. Kukovec, O. V. Maltsev, C. Ruckebusch, L. Hintermann et al., Deciphering the Protonation and Tautomeric Equilibria of Firefly Oxyluciferin by Molecular Engineering and Multivariate Curve Resolution, Chem. Sci, vol.2013, issue.4, pp.3803-3809
URL : https://hal.archives-ouvertes.fr/hal-00861300

A. Ghose, M. Rebarz, O. V. Maltsev, L. Hintermann, C. Ruckebusch et al., Emission Properties of Oxyluciferin and Its Derivatives in Water: Revealing the Nature of the Emissive Species in Firefly Bioluminescence, J. Phys. Chem. B, issue.6, pp.2638-2649, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01141582

A. Ghose, O. V. Maltsev, N. Humbert, L. Hintermann, Y. Arntz et al., Oxyluciferin Derivatives: A Toolbox of Environment-Sensitive Fluorescence Probes for Molecular and Cellular Applications, J. Phys. Chem. B, vol.2017, issue.7, pp.1566-1575

G. Orlova, J. D. Brovko, and L. Y. , Theoretical Study of the Amazing Firefly Bioluminescence: The Formation and Structures of the Light Emitters, J. Am. Chem. Soc, vol.125, pp.6962-6971, 2003.

I. Navizet, D. Roca-sanjuán, L. Yue, Y. Liu, N. Ferré et al., Are the Bio-and Chemiluminescence States of the Firefly Oxyluciferin the Same as the Fluorescence State?, Photochem. Photobiol, vol.89, issue.2, pp.319-325, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00751875

M. Hiyama, H. Akiyama, and N. Koga, Theoretical Insights into the Effect of pH Values on Oxidation Processes in the Emission of Firefly Luciferin in Aqueous Solution, Luminescence, vol.2017, issue.6, pp.1100-1108

M. Hiyama, H. Akiyama, T. Mochizuki, K. Yamada, and N. Koga, Analysis of Photoexcitation Energy Dependence in the Photoluminescence of Firefly Luciferin, Photochem. Photobiol, vol.90, issue.4, 2014.

Y. Noguchi, M. Hiyama, M. Shiga, O. Sugino, and H. Akiyama, Reverse Stability of Oxyluciferin Isomers in Aqueous Solutions, J. Phys. Chem. B, issue.34, pp.8776-8783, 2016.

M. Hiyama, H. Akiyama, K. Yamada, and N. Koga, Theoretical Study of Firefly Luciferin pKa Values-Relative Absorption Intensity in Aqueous Solutions, Photochem. Photobiol, vol.89, issue.3, pp.571-578, 2013.

M. Hiyama, T. Mochizuki, H. Akiyama, and N. Koga, Analysis of Oxyluciferin Photoluminescence Pathways in Aqueous Solutions, Photochem. Photobiol, vol.91, issue.1, pp.74-83, 2015.

T. Yang and J. D. Goddard, Predictions of the Geometries and Fluorescence Emission Energies of Oxyluciferins, J. Phys. Chem. A, vol.111, pp.4489-4497, 2007.

M. Hiyama, Y. Noguchi, H. Akiyama, K. Yamada, and N. Koga, Vibronic Structures in Absorption and Fluorescence Spectra of Firefly Oxyluciferin in Aqueous Solutions, Photochem. Photobiol, vol.91, issue.4, pp.819-827, 2015.

E. Coccia, D. Varsano, and L. Guidoni, Theoretical S1?S0 Absorption Energies of the Anionic Forms of Oxyluciferin by Variational Monte Carlo and Many-Body Green's Function Theory, J. Chem. Theory Comput, vol.13, issue.9, pp.4357-4367, 2017.

O. Falklöf and B. Durbeej, Distinguishing between Keto-Enol and Acid-Base Forms of Firefly Oxyluciferin through Calculation of Excited-State Equilibrium Constants, J. Comput. Chem, issue.30, pp.2184-2194, 2014.

M. Hiyama, M. Shiga, N. Koga, O. Sugino, H. Akiyama et al., The Effect of Dynamical Fluctuations of Hydration Structures on the Absorption Spectra of Oxyluciferin Anions in an Aqueous Solution, Phys. Chem. Chem. Phys, vol.19, issue.15, pp.10028-10035, 2017.

D. A. Case, V. Babin, J. T. Berryman, R. M. Betz, Q. Cai et al., , 2014.

W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, Comparison of Simple Potential Functions for Simulating Liquid Water, J. Chem. Phys, vol.79, issue.2, pp.926-935, 1983.

H. J. Berendsen, J. P. Postma, W. F. Gunsteren, A. Van;-dinola, and J. R. Haak, Molecular Dynamics with Coupling to an External Bath, J. Chem. Phys, p.3684, 1984.

A. Becke, Becke's Three Parameter Hybrid Method Using the LYP Correlation Functional, J. Chem. Phys, vol.98, pp.5648-5652, 1993.

P. J. Stephens, F. J. Devlin, C. F. Chabalowski, and M. J. Frisch, Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields, J. Phys. Chem, vol.98, pp.11623-11627, 1994.

C. Lee, W. Yang, and R. G. Parr, Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron Density, Phys. Rev. B, vol.37, pp.785-789, 1988.

R. Berraud-pache and I. Navizet, QM/MM Calculations on a Newly Synthesised Oxyluciferin Substrate: New Insights into the Conformational Effect, Phys. Chem. Chem. Phys, vol.2016, issue.39, pp.27460-27467
URL : https://hal.archives-ouvertes.fr/hal-01496834

C. Min, A. Ren, J. Guo, Z. Li, L. Zou et al., A TimeDependent Density Functional Theory Investigation on the Origin of Red Chemiluminescence, ChemPhysChem, vol.2010, issue.1, pp.251-259

C. Min and . Leng,

X. Huang,

. Ai-minren, Modification of Firefly Cyclic Amino Oxyluciferin Analogues Emitting Multicolor Light for OLED and nearInfrared Biological Window Light for Bioluminescence Imaging: A Theoretical Study, J. Photochem. Photobiol. A Chem, vol.336, pp.115-122, 2017.

M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Robb, J. R. Cheeseman et al., , 2009.

N. Ferré and J. G. Ángyán, Approximate Electrostatic Interaction Operator for QM/MM Calculations, Chem. Phys. Lett, vol.356, issue.3-4, pp.331-339, 2002.

J. W. Ponder and . Tinker, Software Tools for Molecular Design, Version 6.3. Department of Biochemistry and Molecular Biophysics, 2004.

F. Melaccio, M. Olivucci, R. Lindh, and N. Ferré, Unique QM/MM Potential Energy Surface Exploration Using Microiterations, Int. J. Quantum Chem, issue.13, pp.3339-3346, 2011.
DOI : 10.1002/qua.23067
URL : https://hal.archives-ouvertes.fr/hal-01415208

A. Ren and J. D. Goddard, Predictions of the Electronic Absorption and Emission Spectra of Luciferin and Oxyluciferins Including Solvation Effects, J. Photochem. Photobiol. B Biol, vol.81, issue.3, pp.163-170, 2005.

N. Nakatani, J. Hasegawa, and H. Nakatsuji, Red Light in Chemiluminescence and Yellow-Green Light in Bioluminescence: Color-Tuning Mechanism of Firefly, Photinus Pyralis, Studied by the Symmetry-Adapted Cluster?Configuration Interaction Method, J. Am. Chem. Soc, vol.129, pp.8756-8765, 2007.

B. F. Milne, Red-Shifting the Optical Response of Firefly Oxyluciferin with Group 15/16 Substitutions, Phys. Chem. Chem. Phys, vol.2014, issue.45, pp.24971-24977