Molecular Mechanisms of Photosynthesis, 2014. ,
DOI : 10.1002/9780470758472
Chemistry and Biology of Vision, Journal of Biological Chemistry, vol.20, issue.3, pp.1612-1619, 2012. ,
DOI : 10.1001/archophthalmol.2010.245
Computer simulation of photoinduced molecular motion and reactivity, International Journal of Photoenergy, vol.4, issue.2, pp.57-68, 2002. ,
DOI : 10.1155/S1110662X02000107
Conical Intersections:?? The New Conventional Wisdom, The Journal of Physical Chemistry A, vol.105, issue.26, pp.6277-6293, 2001. ,
DOI : 10.1021/jp003731u
How Nature Harvests Sunlight, Physics Today, vol.21, issue.8, pp.28-34, 1997. ,
DOI : 10.1063/1.1699044
-Hydroxyphenyl-(1,3,5)-triazine, The Journal of Physical Chemistry A, vol.109, issue.33, pp.7527-7537, 2005. ,
DOI : 10.1021/jp051108+
Conical intersection dynamics of the primary photoisomerization event in vision, Nature, vol.274, issue.7314, pp.440-443, 2010. ,
DOI : 10.1038/nature09346
Pre-Lumirhodopsin and the Bleaching of Visual Pigments, Nature, vol.39, issue.4874, pp.1279-1286, 1963. ,
DOI : 10.1042/bj0450304
Rhodopsin Emission in Real Time:?? A New Aspect of the Primary Event in Vision, Journal of the American Chemical Society, vol.120, issue.37 ,
DOI : 10.1021/ja981659w
The first step in vision: femtosecond isomerization of rhodopsin, Science, vol.254, issue.5030, pp.412-415, 1991. ,
DOI : 10.1126/science.1925597
Local vibrational coherences drive the primary photochemistry of vision, Nature Chemistry, vol.66, issue.12, pp.980-986, 2015. ,
DOI : 10.1109/PROC.1978.10837
The Primary Photochemistry of Vision Occurs at the Molecular Speed Limit, The Journal of Physical Chemistry B, vol.121, issue.16, pp.4040-4047, 2017. ,
DOI : 10.1021/acs.jpcb.7b02329
Xanthorhodopsin: A bacteriorhodopsin-like proton pump with a carotenoid antenna, Biochimica et Biophysica Acta (BBA) - Bioenergetics, vol.1777, issue.7-8, pp.684-688, 2008. ,
DOI : 10.1016/j.bbabio.2008.05.005
Proton transfers in the bacteriorhodopsin photocycle, Biochimica et Biophysica Acta (BBA) - Bioenergetics, vol.1757, issue.8, pp.1012-1018, 2006. ,
DOI : 10.1016/j.bbabio.2005.11.003
Direct observation of the femtosecond excited-state cis-trans isomerization in bacteriorhodopsin, Science, vol.240, issue.4853, pp.777-779, 1988. ,
DOI : 10.1126/science.3363359
Microbial and Animal Rhodopsins: Structures, Functions, and Molecular Mechanisms, Chemical Reviews, vol.114, issue.1, pp.126-163, 2014. ,
DOI : 10.1021/cr4003769
URL : https://doi.org/10.1021/cr4003769
Model systems for understanding absorption tuning by opsin proteins, Chemical Society Reviews, vol.96, issue.4, pp.913-924, 2008. ,
DOI : 10.1113/jphysiol.1990.sp018082
Comparative investigation of the photoisomerization of the protonated and unprotonated n-butylamine Schiff bases of 9-cis-, 11-cis-, 13-cis-, and all-trans-retinals, Journal of the American Chemical Society, vol.108, issue.6, pp.1245-1251, 1986. ,
DOI : 10.1021/ja00266a020
Bacteriorhodopsin: mutating a biomaterial into an optoelectronic material, Applied Microbiology and Biotechnology, vol.53, issue.6, pp.633-639, 2000. ,
DOI : 10.1007/s002539900311
Atomistic design of microbial opsin-based blue-shifted optogenetics tools, Nature Communications, vol.48, pp.10-1038 ,
DOI : 10.1021/bi901338d
A Blue-shifted Light-driven Proton Pump for Neural Silencing, Journal of Biological Chemistry, vol.75, issue.28, pp.20624-20632, 2013. ,
DOI : 10.1038/nmeth0611-447
An ab Initio Minimal Model for Retinal Photoisomerization, Journal of the American Chemical Society, vol.119, issue.23, pp.6891-6901, 1997. ,
Structure, Spectroscopy, and Spectral Tuning of the Gas-Phase Retinal Chromophore:?? The ??-Ionone ???Handle??? and Alkyl Group Effect, The Journal of Physical Chemistry A, vol.109, issue.29, pp.6597-6605, 2005. ,
DOI : 10.1021/jp052068c
About the intrinsic photochemical properties of the 11-cis retinal chromophore: computational clues for a trap state and a lever effect in Rhodopsin catalysis, Theoretical Chemistry Accounts, vol.33, issue.1, pp.173-183, 2007. ,
DOI : 10.1002/ijch.199500026
Geometries and Vertical Excitation Energies in Retinal Analogues Resolved at the CASPT2 Level of Theory: Critical Assessment of the Performance of CASSCF, CC2, and DFT Methods, Journal of Chemical Theory and Computation, vol.9, issue.11, pp.4915-4927, 2013. ,
DOI : 10.1021/ct400423u
Proton Transfer in Bacteriorhodopsin:?? Structure, Excitation, IR Spectra, and Potential Energy Surface Analyses by an ab Initio QM/MM Method, The Journal of Physical Chemistry B, vol.104, issue.45, pp.10678-10691, 2000. ,
DOI : 10.1021/jp001508r
Probing the Rhodopsin Cavity with Reduced Retinal Models at the CASPT2//CASSCF/AMBER Level of Theory, Journal of the American Chemical Society, vol.125, issue.23, pp.6868-6869, 2003. ,
DOI : 10.1021/ja035087d
Calculating Absorption Shifts for Retinal Proteins:?? Computational Challenges, The Journal of Physical Chemistry B, vol.109, issue.8, pp.3606-3615, 2005. ,
DOI : 10.1021/jp0463060
Theoretical Studies on the Color-Tuning Mechanism in Retinal Proteins, Journal of Chemical Theory and Computation, vol.3, issue.2, pp.605-618, 2007. ,
DOI : 10.1021/ct6002687
An Opsin Shift in Rhodopsin:?? Retinal S0???S1 Excitation in Protein, in Solution, and in the Gas Phase, Journal of the American Chemical Society, vol.129, issue.43, pp.13035-13042, 2007. ,
DOI : 10.1021/ja0732126
Molecular Dynamics Simulation of Bacteriorhodopsin's Photoisomerization Using Ab Initio Forces for the Excited Chromophore, Biophysical Journal, vol.85, issue.3, pp.1440-1449, 2003. ,
DOI : 10.1016/S0006-3495(03)74576-7
Solvent and Protein Effects on the Structure and Dynamics of the Rhodopsin Chromophore, ChemPhysChem, vol.109, issue.9, pp.1836-1847, 2005. ,
DOI : 10.1002/ijch.199500032
Tracking the excited-state time evolution of the visual pigment with multiconfigurational quantum chemistry, Proc. Natl. Acad ,
DOI : 10.1021/jp972752u
Modelling retinal chromophores photoisomerization: from minimal models in vacuo to ultimate bidimensional spectroscopy in rhodopsins, Phys. Chem. Chem. Phys., vol.5, issue.32, pp.16865-16888, 2014. ,
DOI : 10.1021/jz5002314
URL : https://hal.archives-ouvertes.fr/hal-01121384
Direct QM/MM Excited-State Dynamics of Retinal Protonated Schiff Base in Isolation and Methanol Solution, The Journal of Physical Chemistry B, vol.119, issue.3, pp.704-714, 2015. ,
DOI : 10.1021/jp5038798
Second???order perturbation theory with a complete active space self???consistent field reference function, The Journal of Chemical Physics, vol.23, issue.2, pp.1218-1226, 1992. ,
DOI : 10.1016/0009-2614(91)90407-Z
Photoisomerization Path for a Realistic Retinal Chromophore Model:?? The Nonatetraeniminium Cation, Journal of the American Chemical Society, vol.120, issue.6, pp.1285-1288, 1998. ,
DOI : 10.1021/ja972695i
Initial Excited-State Relaxation of the Isolated 11-cis Protonated Schiff Base of Retinal:?? Evidence for in-Plane Motion from ab Initio Quantum Chemical Simulation of the Resonance Raman Spectrum, Journal of the American Chemical Society, vol.121, issue.5, pp.1023-1029, 1999. ,
DOI : 10.1021/ja981719y
Computational Organic Photochemistry: Strategy, Achievements and Perspectives, Theoretical Chemistry Accounts, vol.101, issue.21, pp.87-105, 2006. ,
DOI : 10.1002/ijch.196900034
Computational evidence in favor of a two-state, two-mode model of the retinal chromophore photoisomerization, Proceedings of the National Academy of Sciences, vol.158, issue.15, pp.9379-9384, 2000. ,
DOI : 10.1016/0301-0104(91)87074-6
Femtosecond Polarized Pump???Probe and Stimulated Emission Spectroscopy of the Isomerization Reaction of Rhodopsin, The Journal of Physical Chemistry A, vol.103, issue.14 ,
DOI : 10.1021/jp9832847
Photoisomerization Dynamics of a Simple Retinal Chromophore Model, Journal of the American Chemical Society, vol.119, issue.51, pp.12687-12688, 1997. ,
DOI : 10.1021/ja9725763
From The Cover: The retinal chromophore/chloride ion pair: Structure of the photoisomerization path and interplay of charge transfer and covalent states, Proceedings of the National Academy of Sciences, vol.105, issue.52 ,
DOI : 10.1021/jp010704a
Counterion Controlled Photoisomerization of Retinal Chromophore Models:?? a Computational Investigation, Journal of the American Chemical Society, vol.126, issue.49, pp.16018-16037, 2004. ,
DOI : 10.1021/ja048782+
Electrostatic Control of the Photoisomerization Efficiency and Optical Properties in Visual Pigments: On the Role of Counterion Quenching, Journal of the American Chemical Society, vol.131, issue.14, pp.5172-5186, 2009. ,
DOI : 10.1021/ja808424b
The Retinal Conformation and its Environment in Rhodopsin in Light of a New 2.2?? Crystal Structure, Journal of Molecular Biology, vol.342, issue.2, pp.571-583, 2004. ,
DOI : 10.1016/j.jmb.2004.07.044
Structure of bacteriorhodopsin at 1.55 ?? resolution, Journal of Molecular Biology, vol.291, issue.4, pp.899-911, 1999. ,
DOI : 10.1006/jmbi.1999.3027
Insights for Light-Driven Molecular Devices from ab initio Multiple Spawning Excited-State Dynamics of Organic and Biological Chromophores, ChemInform, vol.39, issue.18, pp.119-126, 2006. ,
DOI : 10.1002/chin.200618276
Complete-active-space self-consistent-field/Amber parameterization of the Lys296?retinal?Glu113 rhodopsin chromophore-counterion system, Theoretical Chemistry Accounts, vol.112, pp.335-341, 2004. ,
Product formation in rhodopsin by fast hydrogen motions, Physical Chemistry Chemical Physics, vol.49, issue.9, pp.3645-3648, 2011. ,
DOI : 10.1002/anie.200905061
The dynamics of the primary event in rhodopsins revisited, Chemical Physics, vol.158, issue.2-3, pp.303-314, 1991. ,
DOI : 10.1016/0301-0104(91)87074-6
Bicycle-pedal model for the first step in the vision process, Nature, vol.197, issue.5553, pp.679-683, 1976. ,
DOI : 10.1017/S0033583500001785
Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme, Journal of Molecular Biology, vol.103, issue.2, pp.227-249, 1976. ,
DOI : 10.1016/0022-2836(76)90311-9
A tunable QM/MM approach to chemical reactivity, structure and physico-chemical properties prediction, Theoretical Chemistry Accounts, vol.105, issue.1, pp.219-240, 2007. ,
DOI : 10.1007/s00214-007-0275-9
Structure, initial excited-state relaxation, and energy storage of rhodopsin resolved at the multiconfigurational perturbation theory level, Proceedings of the National Academy of Sciences, vol.124, issue.17, pp.17908-17913, 2004. ,
DOI : 10.1021/ja012666e
The role of HOOP-modes in the ultrafast photo-isomerization of retinal models. Chemical Physics. Electron Correlation and Molecular Dynamics for Excited States and Photochemistry 349, pp.348-355, 2008. ,
Structural Observation of the Primary Isomerization in Vision with Femtosecond-Stimulated Raman, Science, vol.310, issue.5750, pp.1006-1009, 2005. ,
DOI : 10.1126/science.1118379
Non-adiabatic dynamics close to conical intersections and the surface hopping perspective, Frontiers in Chemistry, vol.121, issue.39, p.35, 2014. ,
DOI : 10.1063/1.1793991
Physical chemistry: Seaming is believing, Nature, vol.104, issue.7314, pp.412-413, 2010. ,
DOI : 10.1038/467412a
Comparison of algorithms for conical intersection optimisation using semiempirical methods, Theoretical Chemistry Accounts, vol.34, issue.5-6, pp.837-844, 2007. ,
DOI : 10.1007/s002149900083
A direct method for the location of the lowest energy point on a potential surface crossing, Chemical Physics Letters, vol.223, issue.3, pp.269-274, 1994. ,
DOI : 10.1016/0009-2614(94)00433-1
Molecular dynamics with electronic transitions, The Journal of Chemical Physics, vol.76, issue.2, pp.1061-1071, 1990. ,
DOI : 10.1002/qua.560320105
Perspective: Nonadiabatic dynamics theory, The Journal of Chemical Physics, vol.2, issue.22, pp.22-301, 2012. ,
DOI : 10.1063/1.4742066
URL : http://aip.scitation.org/doi/pdf/10.1063/1.4757762
Inhomogeneous Electron Gas, Physical Review, vol.80, issue.3B, pp.864-871, 1964. ,
DOI : 10.1088/0370-1328/80/5/307
Self-Consistent Equations Including Exchange and Correlation Effects, Physical Review, vol.119, issue.4A, pp.1133-1138, 1965. ,
DOI : 10.1103/PhysRev.119.1153
Density-Functional Theory for Time-Dependent Systems, Physical Review Letters, vol.140, issue.12, pp.997-1000, 1984. ,
DOI : 10.1103/PhysRev.140.A1133
TD-DFT Performance for the Visible Absorption Spectra of Organic Dyes:?? Conventional versus Long-Range Hybrids, Journal of Chemical Theory and Computation, vol.4, issue.1, pp.123-135, 2008. ,
DOI : 10.1021/ct700187z
Regarding the use and misuse of retinal protonated Schiff base photochemistry as a test case for time-dependent density-functional theory, The Journal of Chemical Physics, vol.142, issue.14, pp.144104-144145, 2015. ,
DOI : 10.1021/jp0463060
URL : https://hal.archives-ouvertes.fr/hal-01651410
Intramolecular photo-induced charge transfer in visual retinal chromophore mimics: electron density-based indices at the TD-DFT and post-HF levels, Theoretical Chemistry Accounts, vol.109, issue.305, p.96, 2016. ,
DOI : 10.1021/jp0463060
A Qualitative Index of Spatial Extent in Charge-Transfer Excitations, Journal of Chemical Theory and Computation, vol.7, issue.8, pp.2498-2506, 2011. ,
DOI : 10.1021/ct200308m
Second-order perturbation theory with a CASSCF reference function, The Journal of Physical Chemistry, vol.94, issue.14, pp.5483-5488, 1990. ,
DOI : 10.1021/j100377a012
New Developments in Molecular Orbital Theory, Reviews of Modern Physics, vol.46, issue.2, pp.69-89, 1951. ,
DOI : 10.1051/jcp/1949460497
A complete active space SCF method (CASSCF) using a density matrix formulated super-CI approach, Chemical Physics, vol.48, issue.2, pp.157-173, 1980. ,
DOI : 10.1016/0301-0104(80)80045-0
How to select active space for multiconfigurational quantum chemistry?, International Journal of Quantum Chemistry, vol.72, issue.13, pp.3329-3338, 2011. ,
DOI : 10.1021/jo071157d
The restricted active space self-consistent-field method, implemented with a split graph unitary group approach, The Journal of Physical Chemistry, vol.94, issue.14, pp.5477-5482, 1990. ,
DOI : 10.1021/j100377a011
The generalized active space concept in multiconfigurational self-consistent field methods, The Journal of Chemical Physics, vol.3, issue.4, pp.44128-44175, 2011. ,
DOI : 10.1063/1.2953696
Quantum Theory of Many-Particle Systems. I. Physical Interpretations by Means of Density Matrices, Natural Spin-Orbitals, and Convergence Problems in the Method of Configurational Interaction, Physical Review, vol.88, issue.6, pp.1474-1489, 1955. ,
DOI : 10.1103/PhysRev.88.1217
Multiconfiguration perturbation theory with imaginary level shift, Chemical Physics Letters, vol.274, issue.1-3, pp.196-204, 1997. ,
DOI : 10.1016/S0009-2614(97)00669-6
A modified definition of the zeroth-order Hamiltonian in multiconfigurational perturbation theory (CASPT2), Chemical Physics Letters, vol.396, issue.1-3, pp.142-149, 2004. ,
DOI : 10.1016/j.cplett.2004.08.032
The IPEA dilemma in CASPT2, Chemical Science, vol.37, issue.2, pp.1482-1499, 2017. ,
DOI : 10.1002/jcc.24283
The multi-state CASPT2 method, Chemical Physics Letters, vol.288, issue.2-4, pp.299-306, 1998. ,
DOI : 10.1016/S0009-2614(98)00252-8
Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States, Chemical Reviews, vol.115, issue.12, pp.6217-6263, 2015. ,
DOI : 10.1021/cr500628b
Ab Initio NMR Spectra for Molecular Systems with a Thousand and More Atoms: A Linear-Scaling Method, Angewandte Chemie International Edition, vol.43, issue.34, pp.4485-4489, 2004. ,
DOI : 10.1002/anie.200460336
QM/MM Methods for Biomolecular Systems, Angewandte Chemie International Edition, vol.24, issue.462, pp.1198-1229, 2009. ,
DOI : 10.1021/cen-v024n010.p1375
Quantum Mechanics/Molecular Mechanics Approaches in NIC Series. 3: Modern Methods and Algorithms of Quantum Chemistry, pp.285-305, 2000. ,
Quantum mechanical computations on very large molecular systems: The local self-consistent field method, Journal of Computational Chemistry, vol.77, issue.3, pp.269-282, 1994. ,
DOI : 10.1063/1.444375
Generalized Hybrid Orbital (GHO) Method for Combining Ab Initio Hartree???Fock Wave Functions with Molecular Mechanics, The Journal of Physical Chemistry A, vol.108, issue.4, pp.632-650, 2004. ,
DOI : 10.1021/jp036755k
A combinedab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl? exchange reaction and gas phase protonation of polyethers, Journal of Computational Chemistry, vol.107, issue.6, pp.718-730, 1986. ,
DOI : 10.1016/B978-0-12-164720-9.50006-4
A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations, Journal of Computational Chemistry, vol.106, issue.6, pp.700-733, 1990. ,
DOI : 10.1103/PhysRevB.26.4571
MM: what have we learned, where are we, and where do we go from here? Theoretical Chemistry Accounts, pp.185-199, 2007. ,
Development and testing of a general amber force field, Journal of Computational Chemistry, vol.17, issue.9, pp.1157-1174, 2004. ,
DOI : 10.1002/jcc.20035
Chapter 3 Hybrid Methods: ONIOM(QM:MM) and QM/MM, Annual Reports in Computational Chemistry, vol.2, pp.35-51, 2006. ,
DOI : 10.1016/S1574-1400(06)02003-2
Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins, Journal of Chemical Theory and Computation, vol.9, issue.9, pp.4046-4063, 2013. ,
DOI : 10.1021/ct4003702
AmberTools 14 ,
Automatic atom type and bond type perception in molecular mechanical calculations, Journal of Molecular Graphics and Modelling, vol.25, issue.2, pp.247-260, 2006. ,
DOI : 10.1016/j.jmgm.2005.12.005
Comparison of multiple Amber force fields and development of improved protein backbone parameters, Proteins: Structure, Function, and Bioinformatics, vol.43, issue.3, pp.712-725, 2006. ,
DOI : 10.1002/prot.21123
8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table, 8: New Capabilities for Multiconfigurational Quantum Chemical Calculations across the Periodic Table, pp.506-541, 2016. ,
DOI : 10.1002/chem.201100438
URL : https://hal.archives-ouvertes.fr/hal-01639026
Excited state dynamics of bacteriorhodopsin revealed by transient stimulated emission spectra, Chemical Physics Letters, vol.261, issue.4-5, pp.389-395, 1996. ,
DOI : 10.1016/0009-2614(96)01017-2
The photoisomerization of retinal in bacteriorhodopsin: Experimental evidence for a three-state model, Proceedings of the National Academy of Sciences, vol.261, issue.3, pp.15124-15129, 1996. ,
DOI : 10.1016/0009-2614(96)01017-2
Following Evolution of Bacteriorhodopsin in Its Reactive Excited State via Stimulated Emission Pumping, Journal of the American Chemical Society, vol.124, issue.30, pp.8854-8858, 2002. ,
DOI : 10.1021/ja026426q
Probing Ultrafast Photochemistry of Retinal Proteins in the Near-IR: Bacteriorhodopsin and Anabaena Sensory Rhodopsin vs Retinal Protonated Schiff Base in Solution, The Journal of Physical Chemistry B, vol.117, issue.16, pp.4670-4679, 2013. ,
DOI : 10.1021/jp309189y
Femtosecond spectroscopy of the photoisomerisation of the protonated Schiff base of all-trans retinal, Chemical Physics Letters, vol.263, issue.5, pp.613-621, 1996. ,
DOI : 10.1016/S0009-2614(96)01269-9
Ultrafast Excited State Dynamics of the Protonated Schiff Base of All-trans Retinal in Solvents, Biophysical Journal, vol.88, issue.4, pp.2779-2788, 2005. ,
DOI : 10.1529/biophysj.104.046094
Photochemical dynamics of all-trans retinal protonated Schiff-base in solution: Excitation wavelength dependence, Chemical Physics, vol.341, issue.1-3, pp.267-275, 2007. ,
DOI : 10.1016/j.chemphys.2007.06.052
Heterogeneity and Relaxation Dynamics of the Photoexcited Retinal Schiff Base Cation in Solution, The Journal of Physical Chemistry B, vol.113, issue.13, pp.4384-4393, 2009. ,
DOI : 10.1021/jp8077216
Population Branching in the Conical Intersection of the Retinal Chromophore Revealed by Multipulse Ultrafast Optical Spectroscopy, Journal of the American Chemical Society, vol.134, issue.2, pp.955-961, 2012. ,
DOI : 10.1021/ja205763x
Photochemistry of a Retinal Protonated Schiff-Base Analogue Mimicking the Opsin Shift of Bacteriorhodopsin, The Journal of Physical Chemistry B, vol.111, issue.9, pp.2327-2334, 2007. ,
DOI : 10.1021/jp0669308
Backbone Modification of Retinal Induces Protein-like Excited State Dynamics in Solution, Journal of the American Chemical Society, vol.134, issue.20, pp.8318-8320, 2012. ,
DOI : 10.1021/ja3007929
Synthetic Control of Retinal Photochemistry and Photophysics in Solution, Journal of the American Chemical Society, vol.136, issue.6, pp.2650-2658, 2014. ,
DOI : 10.1021/ja4121814
Retinal Protonated Schiff Base in Solution, Journal of the American Chemical Society, vol.137, issue.39, pp.12434-12437, 2015. ,
DOI : 10.1021/jacs.5b06492
Multireference second-order perturbation theory: How size consistent is ???almost size consistent???, The Journal of Chemical Physics, vol.93, issue.4, pp.44105-82, 2005. ,
DOI : 10.1002/(SICI)1097-461X(1999)72:6<549::AID-QUA2>3.0.CO;2-G
Aborted double bicycle-pedal isomerization with hydrogen bond breaking is the primary event of bacteriorhodopsin proton pumping, Proceedings of the National Academy of Sciences, vol.155, issue.4 ,
DOI : 10.1016/0009-2614(89)85347-3
The use of bacteriorhodopsin in optical processing: A review, Journal of Scientific and Industrial Research, vol.54, pp.55-66, 1995. ,
Conversion of bacteriorhodopsin into a chloride ion pump, Science, vol.269, issue.5220, p.95, 1995. ,
DOI : 10.1126/science.7604281
Asymmetric Functional Conversion of Eubacterial Light-driven Ion Pumps, Journal of Biological Chemistry, vol.22, issue.19, pp.9883-9893, 2016. ,
DOI : 10.1021/bi047500f
Engineering an Inward Proton Transport from a Bacterial Sensor Rhodopsin, Journal of the American Chemical Society, vol.131, issue.45, pp.16439-16444, 2009. ,
DOI : 10.1021/ja904855g
Converting a Light-Driven Proton Pump into a Light-Gated Proton Channel, Journal of the American Chemical Society, vol.137, issue.9, pp.3291-3299, 2015. ,
DOI : 10.1021/ja511788f
Protein Design:?? Reengineering Cellular Retinoic Acid Binding Protein II into a Rhodopsin Protein Mimic, Journal of the American Chemical Society, vol.129, issue.19, pp.6140-6148, 2007. ,
DOI : 10.1021/ja067546r
Probing Wavelength Regulation with an Engineered Rhodopsin Mimic and a C15-Retinal Analogue, ChemPlusChem, vol.72, issue.4, pp.273-276, 2012. ,
DOI : 10.1021/bi025636c
Tuning the Electronic Absorption of Protein-Embedded All-trans-Retinal, Science, vol.67, issue.Pt 4, pp.1340-1343, 2012. ,
DOI : 10.1107/S0907444911001314
Molecular Mechanism of Wide Photoabsorption Spectral Shifts of Color Variants of Human Cellular Retinol Binding Protein II, Journal of the American Chemical Society, vol.137, issue.41, pp.13362-13370, 2015. ,
DOI : 10.1021/jacs.5b08316
simulations of two-dimensional electronic spectra: The SOS//QM/MM approach, International Journal of Quantum Chemistry, vol.396, issue.2, pp.85-93, 2014. ,
DOI : 10.1016/j.cplett.2004.08.032
URL : https://hal.archives-ouvertes.fr/hal-01121383
Toward an Understanding of the Retinal Chromophore in Rhodopsin Mimics, The Journal of Physical Chemistry B, vol.117, issue.35, pp.10053-10070 ,
DOI : 10.1021/jp305935t
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald, Journal of Chemical Theory and Computation, vol.9, issue.9, pp.3878-3888, 2013. ,
DOI : 10.1021/ct400314y
MDAnalysis: A toolkit for the analysis of molecular dynamics simulations, Journal of Computational Chemistry, vol.4, issue.Suppl. 2, pp.2319-2327, 2011. ,
DOI : 10.1109/5992.998641
MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations, Proceedings of the 15th Python in Science Conference, pp.98-105, 2016. ,
Toward Automatic Rhodopsin Modeling as a Tool for High-Throughput Computational Photobiology, Journal of Chemical Theory and Computation, vol.12, issue.12, pp.6020-6034, 2016. ,
DOI : 10.1021/acs.jctc.6b00367
URL : https://hal.archives-ouvertes.fr/hal-01409070
Understanding Structure and Function in the Light-Driven Proton Pump Bacteriorhodopsin, Journal of Structural Biology, vol.124, issue.2-3, pp.164-178, 1998. ,
DOI : 10.1006/jsbi.1998.4044
Role of internal water molecules in bacteriorhodopsin, Biochimica et Biophysica Acta (BBA) - Bioenergetics, vol.1460, issue.1, pp.5-272800138, 2000. ,
DOI : 10.1016/S0005-2728(00)00138-9
Water Molecules in the Schiff Base Region of Bacteriorhodopsin, Journal of the American Chemical Society, vol.125, pp.13312-13313, 2003. ,
Hydration switch model for the proton transfer in the Schiff base region of bacteriorhodopsin, Biochimica et Biophysica Acta (BBA) - Bioenergetics, vol.1658, issue.1-2, p.153, 2004. ,
DOI : 10.1016/j.bbabio.2004.03.015
Ultrafast energy relaxation in bacteriorhodopsin studied by time-integrated fluorescence. Phys, Chamistry Chem. Phys, vol.4, pp.5020-5024, 2002. ,
Locked Pigments, The Journal of Physical Chemistry B, vol.103, issue.24, pp.5122-5130, 1999. ,
DOI : 10.1021/jp9846227
Photoselective Ultrafast Investigation of Xanthorhodopsin and Its Carotenoid Antenna Salinixanthin, The Journal of Physical Chemistry B, vol.114, issue.8, pp.3038-3045, 2010. ,
DOI : 10.1021/jp910845h
Origin of Circular Dichroism of Xanthorhodopsin. A Study with Artificial Pigments, The Journal of Physical Chemistry B, vol.119, issue.2, pp.456-464, 2014. ,
DOI : 10.1021/jp510534s
Role of Hydrogen-Bond Network in Energy Storage of Bacteriorhodopsin's Light-Driven Proton Pump Revealed by ab Initio Normal-Mode Analysis, Journal of the American Chemical Society, vol.126, issue.34, pp.47506-155, 2004. ,
DOI : 10.1021/ja047506s
Proton Transfer Pathways in Bacteriorhodopsin at 2.3 Angstrom Resolution, Science, vol.280, issue.5371, pp.1934-1937, 1998. ,
DOI : 10.1126/science.280.5371.1934
Electron-crystallographic Refinement of the Structure of Bacteriorhodopsin, Journal of Molecular Biology, vol.259, issue.3, pp.393-421, 1996. ,
DOI : 10.1006/jmbi.1996.0328
Protein, lipid and water organization in bacteriorhodopsin crystals: a molecular view of the purple membrane at 1.9 ?? resolution, Structure, vol.7, issue.8, pp.909-917, 1999. ,
DOI : 10.1016/S0969-2126(99)80118-X
Complete Identification of C:O Stretching Vibrational Bands of Protonated Aspartic Acid Residues in the Difference Infrared Spectra of M and N Intermediates versus Bacteriorhodopsin, Biochemistry, vol.33, issue.11, pp.178-181, 1994. ,
DOI : 10.1021/bi00177a006
Glutamic Acid 204 is the Terminal Proton Release Group at the Extracellular Surface of Bacteriorhodopsin, Journal of Biological Chemistry, vol.12, issue.45, pp.27122-27128, 1995. ,
DOI : 10.1021/bi00081a010
Hydrogen-bonding changes of internal water molecules upon the actions of microbial rhodopsins studied by FTIR spectroscopy, Biochimica et Biophysica Acta (BBA) - Bioenergetics, vol.1837, issue.5, pp.598-605, 2014. ,
DOI : 10.1016/j.bbabio.2013.09.004
Vibrational spectroscopy of bacteriorhodopsin mutants: chromophore isomerization perturbs trytophan-86, Biochemistry, vol.28, issue.17, p.86 ,
DOI : 10.1021/bi00443a041
Properties of Asp212 to Asn Bacteriorhodopsin Suggest That Asp212 and Asp85 Both Participate in a Counterion and Proton Acceptor Complex near the Schiff Base, The Journal of Biological Chemistry, vol.266, pp.11478-11484, 1991. ,
Aspartic Acid 85 in Bacteriorhodopsin Functions Both as Proton Acceptor and Negative Counterion to the Schiff Base, Journal of Biological Chemistry, vol.267, pp.25730-25733, 1992. ,