Effect of protonation on the isomerization properties of n-butylamine Schiff base of isomeric retinal as revealed by direct HPLC analyses: selection of isomerization pathways by retinal proteins

Mode-Specific Photoresponse of Retinal Protonated Schiff Base Isomers in the Reversible Photochromic Reactions of Microbial and Animal Rhodopsins

The primary photoisomerization reactions of the all-trans to 13-cis and 11-cis to all-trans retinal protonated Schiff base (RPSB) in microbial and animal rhodopsins, respectively, occur on a subpicosecond time scale with high quantum yields. At the same time, the isolated RPSB exhibits slower excited-state decay, in particular, in its all-trans form, and hence the interaction with the protein environment is capable of changing the time scale as well as the specificity of the reaction. Here, by using the high-level QM/MM calculations, we provide a comparative study of the primary photoresponse of cis and trans RPSB isomers in both the initial forms and first photoproducts of microbial Krokinobacter eikastus rhodopsin 2 (KR2) and Halobacterium salinarum bacteriorhodopsin (BR), and animal Bos taurus visual rhodopsin (Rho). By simulating photoabsorption band shapes of RPSB inside the proteins, we show that its photoresponse is highly mode-specific for the forward reactions, resulting in excitation of those vibrational modes that facilitate particular double-bond isomerization. The reverse reaction shows specificity only for 13-cis isomers in microbial rhodopsins, whereas the specificity is lost for all-trans RPSB in visual rhodopsin. This indicates evolutionary highly tuned 11-cis chromophore-protein interactions in visual rhodopsin. We also highlight the differences in the photoresponse of RPSB in two microbial rhodopsins and discuss the implications to their excited-state dynamics.

Study of Photoselectivity in Linear Conjugated Chromophores Using the XMS-CASPT2 Method

Photoisomerization, the structural alteration of molecules upon absorption of light, is crucial for the function of biological chromophores such as retinal in opsins, proteins vital for vision and other light-sensitive processes. The intrinsic selectivity of this isomerization process (i.e., which double bond in the chromophore is isomerized) is governed by both the inherent properties of the chromophore and its surrounding environment. In this study, we employ the extended multistate complete active space second-order perturbation theory (XMS-CASPT2) method to investigate photoisomerization selectivity in linear conjugated chromophores, focusing on two simple molecular models resembling retinal. By analyzing electronic energies, intramolecular charge separation, and conical intersection topographies in the gas phase, we show that the photoproduct formed by rotation around the double bond near the Schiff base is energetically favored. The topographic differences at the conical intersections leading to different photoproducts reveal differences in photodynamics. In multiphoton excitation, the primary photoproduct typically reverts to the initial configuration rather than rotating around a different double bond. Our study offers new insights into the photodynamics of photoisomerizing double bonds in π-conjugated chromophores. We anticipate that our findings will provide valuable perspectives for advancing the understanding of biological chromophores and for designing efficient photochemical switches with applications in molecular electronics and phototherapy.

Photoisomerization pathway of the microbial rhodopsin chromophore in solution

Photoisomerization is a key photochemical reaction in microbial and animal rhodopsins. It is well established that such photoisomerization is highly selective; all-trans to 13-cis, and 11-cis to all-trans forms in microbial and animal rhodopsins, respectively. Nevertheless, unusual photoisomerization pathways have been discovered recently in microbial rhodopsins. In an enzymerhodopsin NeoR, the all-trans chromophore is isomerized into the 7-cis form exclusively, which is stable at room temperature. Although, the 7-cis form is produced by illumination of retinal, formation of the 7-cis form was never reported for a protonated Schiff base of all-trans retinal in solution. Present HPLC analysis of retinal oximes prepared by hydroxylamine reaction revealed that all-trans and 7-cis forms cannot be separated from the syn peaks under the standard HPLC conditions, while it is possible by the analysis of the anti-peaks. Consequently, we found formation of the 7-cis form by the photoreaction of all-trans chromophore in solution, regardless of the protonation state of the Schiff base. Upon light absorption of all-trans protonated retinal Schiff base in solution, excited-state relaxation accompanies double-bond isomerization, producing 7-cis, 9-cis, 11-cis, or 13-cis form. In contrast, specific chromophore-protein interaction enforces selective isomerization into the 13-cis form in many microbial rhodopsins, but into 7-cis in NeoR.

Deconvolution of dynamic heterogeneity in protein structure

Heterogeneity is intrinsic to the dynamic process of a chemical reaction. As reactants are converted to products via intermediates, the nature and extent of heterogeneity vary temporally throughout the duration of the reaction and spatially across the molecular ensemble. The goal of many biophysical techniques, including crystallography and spectroscopy, is to establish a reaction trajectory that follows an experimentally provoked dynamic process. It is essential to properly analyze and resolve heterogeneity inevitably embedded in experimental datasets. We have developed a deconvolution technique based on singular value decomposition (SVD), which we have rigorously practiced in diverse research projects. In this review, we recapitulate the motivation and challenges in addressing the heterogeneity problem and lay out the mathematical foundation of our methodology that enables isolation of chemically sensible structural signals. We also present a few case studies to demonstrate the concept and outcome of the SVD-based deconvolution. Finally, we highlight a few recent studies with mechanistic insights made possible by heterogeneity deconvolution.

Similarities and Differences in Photochemistry of Type I and Type II Rhodopsins

The diversity of the retinal-containing proteins (rhodopsins) in nature is extremely large. Fundamental similarity of the structure and photochemical properties unites them into one family. However, there is still a debate about the origin of retinal-containing proteins: divergent or convergent evolution? In this review, based on the results of our own and literature data, a comparative analysis of the similarities and differences in the photoconversion of the rhodopsin of types I and II is carried out. The results of experimental studies of the forward and reverse photoreactions of the bacteriorhodopsin (type I) and visual rhodopsin (type II) rhodopsins in the femto- and picosecond time scale, photo-reversible reaction of the octopus rhodopsin (type II), photovoltaic reactions, as well as quantum chemical calculations of the forward photoreactions of bacteriorhodopsin and visual rhodopsin are presented. The issue of probable convergent evolution of type I and type II rhodopsins is discussed.

Effects of the Unique Chromophore-Protein Interactions on the Primary Photoreaction of Schizorhodopsin

Schizorhodopsin (SzR) is a newly discovered microbial rhodopsin subfamily, functioning as an unusual inward-proton (H+) pump upon absorbing light. Two major protein structural differences around the chromophore have been found, resulting in unique chromophore-protein interactions that may be responsible for its unusual function. Therefore, it is important to elucidate how such a difference affects the primary photoreaction dynamics. We study the primary dynamics of SzR and its C75S mutant by femtosecond time-resolved absorption (TA) spectroscopy. The obtained TA data revealed that the photoisomerization in SzR proceeds more slowly and less efficiently than typical outward H+-pumping rhodopsins and that it further slows in the C75S mutant. We performed impulsive stimulated Raman measurements to clarify the effect of the cysteine residue on the retinal chromophore and found that interactions with Cys75 flatten the retinal chromophore of wild-type SzR. We discuss the effect of the unique chromophore-cysteine interaction on the retinal isomerization dynamics and structure of SzR.

Photoinduced isomerization sampling of retinal in bacteriorhodopsin

Photoisomerization of retinoids inside a confined protein pocket represents a critical chemical event in many important biological processes from animal vision, nonvisual light effects, to bacterial light sensing and harvesting. Light-driven proton pumping in bacteriorhodopsin entails exquisite electronic and conformational reconfigurations during its photocycle. However, it has been a major challenge to delineate transient molecular events preceding and following the photoisomerization of the retinal from noisy electron density maps when varying populations of intermediates coexist and evolve as a function of time. Here, I report several distinct early photoproducts deconvoluted from the recently observed mixtures in time-resolved serial crystallography. This deconvolution substantially improves the quality of the electron density maps, hence demonstrates that the all-trans retinal undergoes extensive isomerization sampling before it proceeds to the productive 13-cis configuration. Upon light absorption, the chromophore attempts to perform trans-to-cis isomerization at every double bond together with the stalled anti-to-syn rotations at multiple single bonds along its polyene chain. Such isomerization sampling pushes all seven transmembrane helices to bend outward, resulting in a transient expansion of the retinal binding pocket, and later, a contraction due to recoiling. These ultrafast responses observed at the atomic resolution support that the productive photoreaction in bacteriorhodopsin is initiated by light-induced charge separation in the prosthetic chromophore yet governed by stereoselectivity of its protein pocket. The method of a numerical resolution of concurrent events from mixed observations is also generally applicable.

Vibrational coherence and quantum yield of retinal-chromophore-inspired molecular switches

UV-Vis transient absorption (TA) spectroscopy is used to carry out a systematic investigation of the ultrafast CC double photoisomerization dynamics and quantum yield of each isomer of a set of six chromophores based on the same retinal-inspired, indanylidene pyrrolinium (IP) molecular framework.

Intrinsic photoisomerization dynamics of protonated Schiff-base retinal

The retinal protonated Schiff-base (RPSB) in its all-trans form is found in bacterial rhodopsins, whereas visual rhodopsin proteins host 11-cis RPSB. In both cases, photoexcitation initiates fast isomerization of the retinal chromophore, leading to proton transport, storage of chemical energy or signaling. It is an unsolved problem, to which degree this is due to protein interactions or intrinsic RPSB quantum properties. Here, we report on time-resolved action-spectroscopy studies, which show, that upon photoexcitation, cis isomers of RPSB have an almost barrierless fast 400 fs decay, whereas all-trans isomers exhibit a barrier-controlled slow 3 ps decay. Moreover, formation of the 11-cis isomer is greatly favored for all-trans RPSB when isolated. The very fast photoresponse of visual photoreceptors is thus directly related to intrinsic retinal properties, whereas bacterial rhodopsins tune the excited state potential-energy surface to lower the barrier for particular double-bond isomerization, thus changing both the timescale and specificity of the photoisomerization.

The primary photoresponse of protonated Schiff-base retinal in visual and bacterial rhodopsins is fast sub-ps isomerisation. Here, the authors show that the fast photoisomerization of rhodopsin is related to an intrinsic retinal property, whereas bacterial rhodopsins tune the excited-state potential-energy surface and improve the isomerization timescale and specificity.

Ultrafast photoisomerization of pinacyanol: watching an excited state reaction transiting from barrier to barrierless forms

Photoisomerization of 1,1′-diethyl-2,2′-carbocyanine iodide (pinacyanol) in alcohols was investigated by means of femtosecond time-resolved absorption spectroscopy.

Characterizing rhodopsin signaling by EPR spectroscopy: from structure to dynamics

Electron paramagnetic resonance (EPR) spectroscopy, together with spin labeling techniques, has played a major role in the characterization of rhodopsin, the photoreceptor protein and G protein-coupled receptor (GPCR) in rod cells. Two decades ago, these biophysical tools were the first to identify transmembrane helical movements in rhodopsin upon photo-activation, a critical step in the study of GPCR signaling. EPR methods were employed to identify functional loop dynamics within rhodopsin, to measure light-induced millisecond timescale changes in rhodopsin conformation, to characterize the effects of partial agonists on the apoprotein opsin, and to study lipid interactions with rhodopsin. With the emergence of advanced pulsed EPR techniques, the stage was set to determine the amplitude of structural changes in rhodopsin and the dynamics in the rhodopsin signaling complexes. Work in this area has yielded invaluable information about mechanistic properties of GPCRs. Using EPR techniques, receptors are studied in native-like membrane environments and the effects of lipids on conformational equilibria can be explored. This perspective addresses the impact of EPR methods on rhodopsin and GPCR structural biology, highlighting historical discoveries made with spin labeling techniques, and outlining exciting new directions in the field.

Time-resolved structural studies with serial crystallography: A new light on retinal proteins

Structural information of the different conformational states of the two prototypical light-sensitive membrane proteins, bacteriorhodopsin and rhodopsin, has been obtained in the past by X-ray cryo-crystallography and cryo-electron microscopy. However, these methods do not allow for the structure determination of most intermediate conformations. Recently, the potential of X-Ray Free Electron Lasers (X-FELs) for tracking the dynamics of light-triggered processes by pump-probe serial femtosecond crystallography has been demonstrated using 3D-micron-sized crystals. In addition, X-FELs provide new opportunities for protein 2D-crystal diffraction, which would allow to observe the course of conformational changes of membrane proteins in a close-to-physiological lipid bilayer environment. Here, we describe the strategies towards structural dynamic studies of retinal proteins at room temperature, using injector or fixed-target based serial femtosecond crystallography at X-FELs. Thanks to recent progress especially in sample delivery methods, serial crystallography is now also feasible at synchrotron X-ray sources, thus expanding the possibilities for time-resolved structure determination.

Photoisomerization action spectrum of retinal protonated Schiff base in the gas phase

The photophysical behaviour of the isolated retinal protonated n-butylamine Schiff base (RPSB) is investigated in the gas phase using a combination of ion mobility spectrometry and laser spectroscopy. The RPSB cations are introduced by electrospray ionisation into an ion mobility mass spectrometer where they are exposed to tunable laser radiation in the region of the S1 ← S0 transition (420-680 nm range). Four peaks are observed in the arrival time distribution of the RPSB ions. On the basis of predicted collision cross sections with nitrogen gas, the dominant peak is assigned to the all-trans isomer, whereas the subsidiary peaks are assigned to various single, double and triple cis geometric isomers. RPSB ions that absorb laser radiation undergo photoisomerization, leading to a detectable change in their drift speed. By monitoring the photoisomer signal as a function of laser wavelength an action spectrum, extending from 480 to 660 nm with a clear peak at 615 ± 5 nm, is obtained. The photoisomerization action spectrum is related to the absorption spectrum of isolated retinal RPSB molecules and should help benchmark future electronic structure calculations.

Photoisomerization action spectroscopy: flicking the protonated merocyanine–spiropyran switch in the gas phase

Molecular ions drifting through buffer gas are exposed to tunable laser light causing a detectable change in their collision cross section and arrival time at the ion detector. The effect can be exploited to obtain action electronic spectra for selected molecular isomers in the gas phase.

Retinal shows its true colours: photoisomerization action spectra of mobility-selected isomers of the retinal protonated Schiff base

Isomers of the retinal protonated Schiff base are separated and probed using laser radiation in a tandem ion mobility spectrometer yielding isomer-specific electronic spectra.

Bistable retinal schiff base photodynamics of histidine kinase rhodopsin HKR1 from Chlamydomonas reinhardtii

The photodynamics of the recombinant rhodopsin fragment of the histidine kinase rhodopsin HKR1 from Chlamydomonas reinhardtii was studied by absorption and fluorescence spectroscopy. The retinal cofactor of HKR1 exists in two Schiff base forms RetA and RetB. RetA is the deprotonated 13-cis-retinal Schiff base (RSB) absorbing in the UVA spectral region. RetB is the protonated all-trans RSB absorbing in the blue spectral region. Blue light exposure converts RetB fully to RetA. UVA light exposure converts RetA to RetB and RetB to RetA giving a mixture determined by their absorption cross sections and their conversion efficiencies. The quantum efficiencies of conversion of RetA to RetB and RetB to RetA were determined to be 0.096 ± 0.005 and 0.405 ± 0.01 respectively. In the dark thermal equilibration between RetA and RetB with dominant RetA content occurred with a time constant of about 3 days at room temperature. The fluorescence emission behavior of RetA and RetB was studied, and fluorescence quantum yields of ϕ(F) (RetA) = 0.00117 and ϕ(F) (RetB) = 9.4 × 10(-5) were determined. Reaction coordinate schemes of the photodynamics are developed.

Analysis of LhcSR3, a protein essential for feedback de-excitation in the green alga Chlamydomonas reinhardtii

In photosynthetic organisms, feedback dissipation of excess absorbed light energy balances harvesting of light with metabolic energy consumption. This mechanism prevents photodamage caused by reactive oxygen species produced by the reaction of chlorophyll (Chl) triplet states with O₂. Plants have been found to perform the heat dissipation in specific proteins, binding Chls and carotenoids (Cars), that belong to the Lhc family, while triggering of the process is performed by the PsbS subunit, needed for lumenal pH detection. PsbS is not found in algae, suggesting important differences in energy-dependent quenching (qE) machinery. Consistent with this suggestion, a different Lhc-like gene product, called LhcSR3 (formerly known as LI818) has been found to be essential for qE in Chlamydomonas reinhardtii. In this work, we report the production of two recombinant LhcSR isoforms from C. reinhardtii and their biochemical and spectroscopic characterization. We found the following: (i) LhcSR isoforms are Chl a/b- and xanthophyll-binding proteins, contrary to higher plant PsbS; (ii) the LhcSR3 isoform, accumulating in high light, is a strong quencher of Chl excited states, exhibiting a very fast fluorescence decay, with lifetimes below 100 ps, capable of dissipating excitation energy from neighbor antenna proteins; (iii) the LhcSR3 isoform is highly active in the transient formation of Car radical cation, a species proposed to act as a quencher in the heat dissipation process. Remarkably, the radical cation signal is detected at wavelengths corresponding to the Car lutein, rather than to zeaxanthin, implying that the latter, predominant in plants, is not essential; (iv) LhcSR3 is responsive to low pH, the trigger of non-photochemical quenching, since it binds the non-photochemical quenching inhibitor dicyclohexylcarbodiimide, and increases its energy dissipation properties upon acidification. This is the first report of an isolated Lhc protein constitutively active in energy dissipation in its purified form, opening the way to detailed molecular analysis. Owing to its protonatable residues and constitutive excitation energy dissipation, this protein appears to merge both pH-sensing and energy-quenching functions, accomplished respectively by PsbS and monomeric Lhcb proteins in plants.

Photoisomerization of a maleonitrile-type salen Schiff base and its application in fine-tuning infinite coordination polymers

Strategically designed salen ligand 2,3-bis[4-(di-p-tolylamino)-2-hydroxybenzylideneamino]maleonitrile (1), which has pronounced excited-state charge-transfer properties, shows a previously unrecognized form of photoisomerization. On electronic excitation (denoted by an asterisk), 1Z*-->1E isomerization takes place by rotation about the C2--C3 bond, which takes on single-bond character due to the charge-transfer reaction. The isomerization takes place nonadiabatically from the excited-state (1Z) to the ground-state (1E) potential-energy surface in the singlet manifold; 1Z and 1E are neither thermally inconvertible at ambient temperature (25-30 degrees C), nor does photoinduced reverse 1E*-->1Z (or 1Z*) isomerization occur. Isomers 1Z and 1E show very different coordination chemistry towards a Zn(II) precursor. More prominent coordination chemistry is evidenced by a derivative of 1 bearing a carboxyl group, namely, N,N'-dicyanoethenebis(salicylideneimine)dicarboxylic acid (2). Applying 2Z and its photoinduced isomer 2E as building blocks, we then demonstrate remarkable differences in morphology (sphere- and needlelike nanostructure, respectively) of their infinite coordination polymers with Zn(II).

Acceleration of the Z to E photoisomerization of penta-2,4-dieniminium by hydrogen out-of-plane motion: theoretical study on a model system of retinal protonated Schiff base

We report the result of comparison between two reaction coordinates [on the potential energy surface of the first excited state (S(1))] produced by CASSCF and these energies recalculated by MRMP2 in the Z to E photoisomerization of penta-2,4-dieniminium (PDI) as the minimal model of the retinal protonated Schiff base (RPSB). One coordinate is the S(1) state minimum-energy-path (MEP) in mass-weighted coordinates from the S(1) vertically excited point, where a strong hydrogen-out-of plane (HOOP) motion is not exhibited. The energy profile of the S(1) MEP at the MRMP2//CASSCF level shows a barrier for the rotation around the reactive C-C and hits the S(1)/S(0) degeneracy space where the central C-C-C-C dihedral angle is distorted by 65 degrees . The other coordinate is an S(1) coordinate obtained by the relaxed scan strategy. The relaxed coordinate along the central C-C-C-C dihedral angle, which we call the HOOP coordinate, shows strong HOOP motion. According to the MRMP2//CASSCF calculation, there is no barrier on the HOOP coordinate. Furthermore, the S(1) to S(0) transition may be possible without the large skeletal deformation by HOOP motion because the HOOP coordinate encounters the S(1)/S(0) degeneracy space where the central C-C-C-C dihedral angle is distorted by only 40 degrees . Consequently, if PDI is a suitable model molecule for the RPSB as often assumed, the 11-cis to all-trans photoisomerization is predicted to be accelerated by the HOOP motion.

Effect of isomer geometry on the steady-state absorption spectra and femtosecond time-resolved dynamics of carotenoids

Steady-state absorption and femtosecond time-resolved optical spectroscopic studies have been carried out on all-trans-beta-carotene, 15,15'-cis-beta-carotene, all-trans-spheroidene, and 13,14-locked-cis-spheroidene. We examine in detail the effect of isomer geometry on the spectroscopic properties and photophysics of the low-lying S(1) (2(1)A(g)(-)) and S(2) (1(1)B(u)(+)) excited states of these molecules. The experiments on 13,14-locked-cis-spheroidene, a molecule incapable of undergoing cis-to-trans isomerization, provide a unique opportunity to examine the role of isomer geometry in controlling excited-state deactivation of carotenoids. The kinetic results have been obtained using both single wavelength transient absorption measurements and global fitting procedures. The overall scheme for the deactivation of these molecules after S(0) --> S(2) photon absorption is decay of S(2) to a vibrationally hot S(1) state, followed by vibrational relaxation within S(1), and finally, S(1) --> S(0) internal conversion back to the ground state. Changes in isomer geometry are shown to lead to small but noticeable alterations in the spectroscopic and kinetic behavior of the molecules. The effects are interpreted in terms of minor alterations in excited-state energy and vibrational coupling upon isomerization that bring about changes in the spectroscopic and kinetic behavior of this biologically important class of pigments.

Photoisomerization mechanism of rhodopsin and 9-cis-rhodopsin revealed by x-ray crystallography

The primary photochemical process of the visual function has been investigated using the three crystallographic models, 11-cis-rhodopsin, all-trans-bathorhodopsin, and the artificial isomeric 9-cis-rhodopsin. Detailed examination of the atomic displacements and dihedral angle changes of the retinal chromophore involved in the interconversion among these isomers suggests the mechanism of isomerization efficiency.

Femtosecond stimulated Raman study of excited-state evolution in bacteriorhodopsin

Femtosecond time-resolved stimulated Raman spectroscopy (FSRS) is used to examine the photoisomerization dynamics in the excited state of bacteriorhodopsin. Near-IR stimulated emission is observed in the FSRS probe window that decays with a 400-600-fs time constant. Additionally, dispersive vibrational lines appear at the locations of the ground-state vibrational frequencies and decay with a 260-fs time constant. The dispersive line shapes are caused by a nonlinear effect we term Raman initiated by nonlinear emission (RINE) that generates vibrational coherence on the ground-state surface. Theoretical expressions for the RINE line shapes are developed and used to fit the spectral and temporal evolution of the spectra. The rapid 260-fs decay of the RINE peak intensity, compared to the slower evolution of the stimulated emission, indicates that the excited-state population moves in approximately 260 fs to a region on the potential energy surface where the RINE signal is attenuated. This loss of RINE signal is best explained by structural evolution of the excited-state population along multiple low-frequency modes that carry the molecule out of the harmonic photochemically inactive Franck-Condon region and into the photochemically active geometry.

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.

Reflection on medium effects on photochemical reactivity

In reexamining medium effects on photochemical reactions, we have emphasized those on unequilibrated excited species such as the Franck-Condon species. Despite recent advances in femtochemistry, such a discussion in molecular photochemistry is uncommon, and the problem remains challenging on account of the extremely short-lived excited species. However, in such cases, a small perturbation resulting from, for example, weak guest-host interactions could turn into a determining factor in dictating the course of a photochemical channel of deactivation. Examples of medium-directed diabatic processes have been examined with this idea in mind. A modified view on rhodopsin photoisomerization is presented along with the consideration that confinement does not necessarily lead to inhibition of reactions of the trapped substrate.