Ultrafast Spectroscopy of the Protonated Schiff Bases of Free and C13C14 Locked Retinals

Impact of protein-chromophore interaction on the retinal excited state and photocycle of Gloeobacter rhodopsin: role of conserved tryptophan residues

The function of microbial as well as mammalian retinal proteins (aka rhodopsins) is associated with a photocycle initiated by light excitation of the retinal chromophore of the protein, covalently bound through a protonated Schiff base linkage. Although electrostatics controls chemical reactions of many organic molecules, attempt to understand its role in controlling excited state reactivity of rhodopsins and, thereby, their photocycle is scarce. Here, we investigate the effect of highly conserved tryptophan residues, between which the all-trans retinal chromophore of the protein is sandwiched in microbial rhodopsins, on the charge distribution along the retinal excited state, quantum yield and nature of the light-induced photocycle and absorption properties of Gloeobacter rhodopsin (GR). Replacement of these tryptophan residues by non-aromatic leucine (W222L and W122L) or phenylalanine (W222F) does not significantly affect the absorption maximum of the protein, while all the mutants showed higher sensitivity to photobleaching, compared to wild-type GR. Flash photolysis studies revealed lower quantum yield of trans-cis photoisomerization in W222L as well as W222F mutants relative to wild-type. The photocycle kinetics are also controlled by these tryptophan residues, resulting in altered accumulation and lifetime of the intermediates in the W222L and W222F mutants. We propose that protein-retinal interactions facilitated by conserved tryptophan residues are crucial for achieving high quantum yield of the light-induced retinal isomerization, and affect the thermal retinal re-isomerization to the resting state.

Spectroscopy and photoisomerization of protonated Schiff-base retinal derivatives in vacuo

The protonated Schiff-base retinal acts as the chromophore in bacteriorhodopsin as well as in rhodopsin. In both cases, photoexcitation initializes fast isomerization which eventually results in storage of chemical energy or signaling. The details of the photophysics for this important chromophore is still not fully understood. In this study, action-absorption spectra and photoisomerization dynamics of three retinal derivatives are measured in the gas phase and compared to that of the protonated Schiff-base retinal. The retinal derivatives include C₉C₁₀trans-locked, C₁₃C₁₄trans-locked and a retinal derivative without the β-ionone ring. The spectroscopy as well as the isomerization speed of the chromophores are altered significantly as a consequence of the steric constraints.

Mechanism of ultrafast non-reactive deactivation of the retinal chromophore in non-polar solvents

Counterion sensitive photodynamics of the retinal chromophore in solution.

Modelling retinal chromophores photoisomerization: from minimal models in vacuo to ultimate bidimensional spectroscopy in rhodopsins

Modelling of retinal photoisomerization in different environments is reviewed and ultimate ultrafast electronic spectroscopy is proposed for obtaining new insights.

Backbone modification of retinal induces protein-like excited state dynamics in solution

The drastically different reactivity of the retinal chromophore in solution compared to the protein environment is poorly understood. Here, we show that the addition of a methyl group to the C═C backbone of all-trans retinal protonated Schiff base accelerates the electronic decay in solution making it comparable to the proton pump bacteriorhodopsin. Contrary to the notion that reaction speed and efficiency are linked, we observe a concomitant 50% reduction in the isomerization yield. Our results demonstrate that minimal synthetic engineering of potential energy surfaces based on theoretical predictions can induce drastic changes in electronic dynamics toward those observed in an evolution-optimized protein pocket.

4,4'-[Ethylenebis(nitrilomethylidyne)]dibenzonitrile

The mol­ecule of the title Schiff base compound, C₁₈H₁₄N₄, lies across a crystallographic inversion centre and adopts an E configuration with respect to the azomethine (C=N) bonds. The imino groups are coplanar with the aromatic rings with a maximum deviation of 0.1574 (12) Å for the N atom. Within the mol­ecule, the planar units are parallel, but extend in opposite directions from the dimethyl­ene bridge. In the crystal structure, pairs of inter­molecular C—H⋯N hydrogen bonds link neighbouring mol­ecules into centrosymmetric dimers with R²₂(10) ring motifs. An inter­esting feature of the crystal structure is the short inter­molecular C⋯C inter­action with a distance of 3.3821 (13) Å, which is shorter than the sum of the van der Waals radius of a carbon atom.

6,6'-Diethoxy-2,2'-[2,2-dimethylpropane-1,3-diylbis(nitrilomethylidyne)]diphenol

In the crystal structure, the title Schiff base compound, C₂₃H₃₀N₂O₄, exhibits crystallographic twofold rotation symmetry. The imino group is coplanar with the aromatic ring with an N—C—C—C torsion angle of -179.72 (9)°. An intra­molecular O—H⋯N hydrogen bond forms a six-membered ring, producing an S(6) ring motif. The dihedral angle between symmetry related benzene rings is 28.05 (5)°. The eth­oxy group makes a C—O—C—C torsion angle of −7.20 (16)° with the benzene ring. The crystal structure is stabilized by inter­molecular C—H⋯π inter­actions.

2,2′-Dihydroxy-3,3′-[(1E,1′E)-hydrazine-1,2-diylidenedimethylidyne]dibenzoic acidN,N-dimethylformamide disolvate

The title compound, C₁₆H₁₂N₂O₆·2C₃H₇NO, lies across a crystallographic inversion centre which is situated at the midpoint of the central N—N bond. The substitution at the C=N bond adopts a trans configuration and it is essentially coplanar with the benzene ring [N—C—C—C torsion angles = −173.9 (4) and 6.4 (6)°]. All torsion angles involving non-H atoms are close to 180°. Intra­molecular O—H⋯O and weak C—H⋯O hydrogen bonds form S(6) and S(5) ring motifs, respectively, while inter­molecular O—H⋯O and weak C—H⋯O hydrogen bonds connect the Schiff base mol­ecule to solvent dimethyl­formamide mol­ecules.

N,N'-Bis(4-chloro-3-fluoro-benzyl-idene)ethane-1,2-diamine

The asymmetric unit of the title Schiff base compound, C₁₆H₁₂Cl₂F₂N₂, contains one half of the centrosymmetric mol­ecule. Mol­ecules related by translation along the a axis form stacks with short inter­molecular C⋯C distances of 3.429 (3) Å. The crystal packing also exhibits short inter­molecular Cl⋯F contacts of 3.087 (1) Å.

N,N'-Bis(3,5-dichloro-benzyl-idene)-ethane-1,2-diamine

The mol-ecule of the title Schiff base compound, C(16)H(12)Cl(4)N(2), lies across an inversion centre and adopts an E configuration with respect to the azomethine C=N bond. The imine groups are coplanar with the aromatic rings. Within the mol-ecule, the planar units are parallel but extend in opposite directions from the dimethyl-ene bridge. In the crystal structure, mol-ecules are linked together by inter-molecular C-H⋯Cl hydrogen bonds along the a axis.

N,N'-Bis(3-chloro-2-fluoro-benzyl-idene)ethane-1,2-diamine

The mol­ecule of the title centrosymmetric Schiff base compound, C₁₆H₁₂Cl₂F₂N₂, adopts an E configuration with respect to the azomethine C=N bond. The imino groups are coplanar with the aromatic rings. Within the mol­ecule, the planar units are parallel, but extend in opposite directions from the dimethyl­ene bridge. An inter­esting feature of the crystal structure is the short inter­molecular Cl⋯F [3.1747 (5) Å] inter­actions, which are shorter than the sum of the van der Waals radii of these atoms. These inter­actions link neighbouring mol­ecules along the b axis. The crystal structure is further stabilized by π–π inter­actions, with a centroid–centroid distance of 3.5244 (4) Å.

N,N'-Bis(4-bromo-2-fluoro-benzyl-idene)ethane-1,2-diamine

The mol­ecule of the title Schiff base compound, C₁₆H₁₂Br₂F₂N₂, lies across a crystallographic inversion centre and adopts an E configuration with respect to the azomethine C=N bonds. The imino groups are coplanar with the aromatic rings. Within the mol­ecule, the planar units are parallel, but extend in opposite directions from the dimethyl­ene bridge. An inter­esting feature of the crystal structure is the short inter­molecular Br⋯F inter­actions [3.2347 (16) Å, which is shorter than the sum of the van der Waals radii of these atoms]. These inter­actions link neighbouring mol­ecules along the c axis. The crystal structure is further stabilized by inter­molecular C—H⋯N hydrogen bonds.

N,N'-Bis(5-bromo-2-hydroxy-benzyl-idene)-2,2-dimethylpropane-1,3-diamine

The crystal structure of the title Schiff base compound, C₁₉H₂₀Br₂N₂O₂, contains two crystallographically independent mol­ecules (A and B) in the asymmetric unit, with similar conformations. Intra­molecular O—H⋯N (× 4) and C—H⋯N (× 5) hydrogen bonds form six- and five-membered rings, producing S(6) and S(5) ring motifs, respectively. One of the N atoms in mol­ecule A acts as a trifurcated acceptor, the rest of the N atoms being bifurcated acceptors. The dihedral angles between the benzene rings in mol­ecules A and B are 47.83 (17) and 61.11 (17)°, respectively. The mol­ecular conformation is stabilized by intra­molecular O—H⋯N and C—H⋯N hydrogen bonds. The short distances between the centroids of the benzene rings [3.7799 (19)–3.890 (2) Å] indicate the existence of π–π inter­actions. In addition, the crystal structure is further stabilized by an inter­molecular C—H⋯O hydrogen bond, C—H⋯π inter­actions, and short inter­molecular Br⋯Br and Br⋯O contacts [3.4786 (5) and 3.149 (3) Å, respectively].

N,N'-Bis(2-iodo-benzyl-idene)ethane-1,2-diamine

The mol-ecule of the title Schiff base compound, C(16)H(14)I(2)N(2), lies across a crystallographic inversion centre. An intra-molecular C-H⋯I hydrogen bond forms a five-membered ring, producing an S(5) ring motif. The C=N bond is coplanar with the benzene ring and adopts a trans configuration. Within the mol-ecule, the planar units are parallel, but extend in opposite directions from the dimethyl-ene bridge. An inter-esting feature of the crystal structure is the short I⋯N [3.2096 (15) Å] inter-action, which is significantly shorter than the sum of the van der Waals radii of these atoms. In the crystal structure, mol-ecules are linked into one-dimensional extended chains along the c axis and also into one-dimensional extended chains along the b axis through short inter-molecular I⋯N inter-actions, forming two-dimensional networks parallel to the bc plane.

N,N'-Bis(3-methoxy-benzyl-idene)ethane-1,2-diamine

The mol-ecule of the title bidentate Schiff base ligand, C(18)H(20)N(2)O(2), has twofold crystallographic rotation symmetry, giving one half-mol-ecule per asymmetric unit. It adopts a twisted E configuration with respect to the azomethine C=N bond. The imino group is coplanar with the aromatic ring. The dihedral angle between the two benzene rings is 69.52 (5)°. The meth-oxy group is coplanar with the benzene ring, as indicated by the C-O-C-C torsion angle of -179.56 (8)°. In the unit cell, mol-ecules are linked together by inter-molecular C-H⋯O hydrogen bonds, forming chains along the a axis; these chains are further stacked down the b axis by both inter-molecular C-H⋯O and C-H⋯π inter-actions.

N,N'-Bis[2-chloro-5-(trifluoro-meth-yl)benzyl-idene]ethane-1,2-diamine

The mol­ecule of the title Schiff base compound, C₁₈H₁₂Cl₂F₆N₂, adopts an E configuration with respect to the azomethine C=N bond. Intra­molecular C—H⋯F (× 2) and C—H⋯Cl (× 2) hydrogen bonds generate S(5) ring motifs. The imino group is coplanar with the aromatic ring. Within the mol­ecule, the planar units are parallel, but extend in opposite directions from the methyl­ene bridge, as indicated by the dihedral angle between the two benzene rings of 3.74 (6)°. The inter­esting features of the crystal structure are weak inter­molecular Cl⋯N and F⋯F inter­actions, with distances of 2.9192 (11) and 3.2714 (10) Å, respectively, which are shorter than the sum of the van der Waals radii of the relevent atoms. These inter­actions link neighbouring mol­ecules into dimers which are stacked down the b axis.

4,4'-Dimethoxy-2,2'-[1,1'-(propane-1,3-diyldinitrilo)diethylidyne]diphenol

In the crystal structure, the title Schiff base compound, C(21)H(26)N(2)O(4), has twofold rotation symmetry. The imino group is coplanar with the aromatic ring. An intra-molecular O-H⋯N hydrogen bond forms a six- membered ring, producing an S(6) ring motif. The two benzene rings are almost perpendicular to each other, making a dihedral angle of 85.00 (2)°. The meth-oxy group is approximately coplanar with the benzene ring, with a C-O-C-C torsion angle of 2.34 (12)°. Neighbouring mol-ecules are linked together by weak inter-molecular C-H⋯O hydrogen bonds and a C-H⋯π inter-action, forming a sheet parallel to the ab plane. The mol-ecules also adopt a zigzag arrangement along the c axis.

Femtobiology

Functions of biologically active molecules are frequently initiated by elementary chemical reactions such as energy and electron transfer, cis-trans isomerizations, and proton transfer. The nature of these reactions generally makes them very fast and efficient, occurring on picosecond and femtosecond timescales. Ultrafast spectroscopy has played an important role in the study of a number of biological processes and has provided unique information about several of nature's responses to light. Here I review the current understanding of light-energy collection and conversion in photosynthesis, the function of carotenoid molecules in photosynthesis, and the primary light-initiated reactions of the photoreceptors rhodopsin, bacteriorhodopsin, photoactive yellow protein, phytochrome, and a new type of blue-light receptor based on flavin chromophores.

N,N'-Bis(3-bromo-benzyl-idene)ethane-1,2-diamine

The mol-ecule of the title Schiff base compound, C(16)H(14)Br(2)N(2), lies across a crystallographic inversion centre. The C=N bond adopts a trans configuration. The imino group is coplanar with the benzene ring. Within the mol-ecule, the planar units are parallel, but extend in opposite directions from the dimethyl-ene bridge. The inter-esting feature of the structure is the weak Br⋯Br inter-action [3.7501 (2) Å] linking the mol-ecules into chains along the c axis. These chains are stacked along the b axis.

N,N'-Bis(4-bromo-benzyl-idene)ethane-1,2-diamine

The mol­ecule of the title Schiff base compound, C₁₆H₁₄Br₂N₂, lies across a crystallographic inversion centre and adopts an E configuration with respect to the azomethine C=N bond. The imino group is coplanar with the aromatic ring. Within the mol­ecule, the planar units are parallel, but extend in opposite directions from the dimethyl­ene bridge. The crystal structure is stabilized by inter­molecular C—H⋯π inter­actions and Br⋯Br [3.6307 (4) Å] short contacts.

Photochemistry of a Retinal Protonated Schiff-Base Analogue Mimicking the Opsin Shift of Bacteriorhodopsin

A retinal Schiff base analogue which artificially mimics the protein-induced red shifting of absorption in bacteriorhodopsin (BR) has been investigated with femtosecond multichannel pump probe spectroscopy. The objective is to determine if the catalysis of retinal internal conversion in the native protein BR, which absorbs at 570 nm, is directly correlated with the protein-induced Stokes shifting of this absorption band otherwise known as the "opsin shift". Results demonstrate that the red shift afforded in the model system does not hasten internal conversion relative to that taking place in a free retinal-protonated Schiff base (RPSB) in methanol solution, and stimulated emission takes place with biexponential kinetics and characteristic timescales of approximately 2 and 10.5 ps. This shows that interactions between the prosthetic group and the protein that lead to the opsin shift in BR are not directly involved in reducing the excited-state lifetime by nearly an order of magnitude. A sub-picosecond phase of spectral evolution, analogues of which are detected in photoexcited retinal proteins and RPSBs in solution, is observed after excitation anywhere within the intense visible absorption band. It consists of a large and discontinuous spectral shift in excited-state absorption and is assigned to electronic relaxation between excited states, a scenario which might also be relevant to those systems as well. Finally, a transient excess bleach component that tunes with the excitation wavelength is detected in the data and tentatively assigned to inhomogeneous broadening in the ground state absorption band. Possible sources of such inhomogeneity and its relevance to native RPSB photochemistry are discussed.

Ultrafast excited state dynamics of the protonated Schiff base of all-trans retinal in solvents

We present a comparative study of the ultrafast photophysics of all-trans retinal in the protonated Schiff base form in solvents with different polarities and viscosities. Steady-state spectra of retinal in the protonated Schiff base form show large absorption-emission Stokes shifts (6500-8100 cm(-1)) for both polar and nonpolar solvents. Using a broadband fluorescence up-conversion experiment, the relaxation kinetics of fluorescence is investigated with 120 fs time resolution. The time-zero spectra already exhibit a Stokes-shift of approximately 6000 cm(-1), indicating depopulation of the Franck-Condon region in < or =100 fs. We attribute it to relaxation along skeletal stretching. A dramatic spectral narrowing is observed on a 150 fs timescale, which we assign to relaxation from the S(2) to the S(1) state. Along with the direct excitation of S(1), this relaxation populates different quasistationary states in S(1), as suggested from the existence of three distinct fluorescence decay times with different decay associated spectra. A 0.5-0.65 ps decay component is observed, which may reflect the direct repopulation of the ground state, in line with the small isomerization yield in solvents. Two longer decay components are observed and are attributed to torsional motion leading to photo-isomerization. The various decay channels show little or no dependence with respect to the viscosity or dielectric constant of the solvents. This suggests that in the protein, the bond selectivity of isomerization is mainly governed by steric effects.

Excited-state dynamics of bacteriorhodopsin probed by broadband femtosecond fluorescence spectroscopy

The impact of varying excitation densities (approximately 0.3 to approximately 40 photons per molecule) on the ultrafast fluorescence dynamics of bacteriorhodopsin has been studied in a wide spectral range (630-900 nm). For low excitation densities, the fluorescence dynamics can be approximated biexponentially with time constants of <0.15 and approximately 0.45 ps. The spectrum associated with the fastest time constant peaks at 650 nm, while the 0.45 ps component is most prominent at 750 nm. Superimposed on these kinetics is a shift of the fluorescence maximum with time (dynamic Stokes shift). Higher excitation densities alter the time constants and their amplitudes. These changes are assigned to multi-photon absorptions.

Counterion Controlled Photoisomerization of Retinal Chromophore Models: a Computational Investigation

CASPT2//CASSCF photoisomerization path computations have been used to unveil the effects of an acetate counterion on the photochemistry of two retinal protonated Schiff base (PSB) models: the 2-cis-penta-2,4-dieniminium and the all-trans-epta-2,4,6-trieniminium cations. Different positions/orientations of the counterion have been investigated and related to (i) the spectral tuning and relative stability of the S0, S1, and S2 singlet states; (ii) the selection of the photochemically relevant excited state; (iii) the control of the radiationless decay and photoisomerization rates; and, finally, (iv) the control of the photoisomerization stereospecificity. A rationale for the results is given on the basis of a simple (electrostatic) qualitative model. We show that the model readily explains the computational results providing a qualitative explanation for different aspects of the experimentally observed "environment" dependent PSB photochemistry. Electrostatic effects likely involved in controlling retinal photoisomerization stereoselectivity in the protein are also discussed under the light of these results, and clues for a stereocontrolled electrostatically driven photochemical process are presented. These computations provide a rational basis for the formulation of a mechanistic model for photoisomerization electrostatic catalysis.

Excited-state singlet manifold and oscillatory features of a nonatetraeniminium retinal chromophore model

In this paper we use ab initio multireference Møller-Plesset second-order perturbation theory computations to map the first five singlet states (S(0), S(1), S(2), S(3), and S(4)) along the initial part of the photoisomerization coordinate for the isolated rhodopsin chromophore model 4-cis-gamma-methylnona-2,4,6,8-tetraeniminium cation. We show that this information not only provides an explanation for the spectral features associated to the chromophore in solution but also, subject to a tentative hypothesis on the effect of the protein cavity, may be employed to explain/assign the ultrafast near-IR excited-state absorption, stimulated emission, and transient excited-state absorption bands observed in rhodopsin proteins (e.g. rhodopsin and bacteriorhodopsin). We also show that the results of vibrational frequency computations reveal a general structure for the first (S(1)) excited-state energy surface of PSBs that is consistent with the existence of the coherent oscillatory motions observed both in solution and in bacteriorhodopsin.