Femtosecond time-resolved fluorescence spectroscopy of bacteriorhodopsin: Direct observation of excited state dynamics in the primary step of the proton pump cycle

Unique Vibrational Characteristics and Structures of the Photoexcited Retinal Chromophore in Ion-Pumping Rhodopsins

Photoisomerization of an all-trans-retinal chromophore triggers ion transport in microbial ion-pumping rhodopsins. Understanding chromophore structures in the electronically excited (S1) state provides insights into the structural evolution on the potential energy surface of the photoexcited state. In this study, we examined the structure of the S1-state chromophore in Natronomonas pharaonis halorhodopsin (NpHR), a chloride ion-pumping rhodopsin, using time-resolved resonance Raman spectroscopy. The spectral patterns of the S1-state chromophore were completely different from those of the ground-state chromophore, resulting from unique vibrational characteristics and the structure of the S1 state. Mode assignments were based on a combination of deuteration shifts of the Raman bands and hybrid quantum mechanics-molecular mechanics calculations. The present observations suggest a weakened bond alternation in the π conjugation system. A strong hydrogen-out-of-plane bending band was observed in the Raman spectra of the S1-state chromophore in NpHR, indicating a twisted polyene structure. Similar frequency shifts for the C═N/C═C and C-C stretching modes of the S1-state chromophore in NpHR were observed in the Raman spectra of sodium ion-pumping and proton-pumping rhodopsins, suggesting that these unique features are common to the S1 states of ion-pumping rhodopsins.

Optical control of ultrafast structural dynamics in a fluorescent protein

The photoisomerization reaction of a fluorescent protein chromophore occurs on the ultrafast timescale. The structural dynamics that result from femtosecond optical excitation have contributions from vibrational and electronic processes and from reaction dynamics that involve the crossing through a conical intersection. The creation and progression of the ultrafast structural dynamics strongly depends on optical and molecular parameters. When using X-ray crystallography as a probe of ultrafast dynamics, the origin of the observed nuclear motions is not known. Now, high-resolution pump-probe X-ray crystallography reveals complex sub-ångström, ultrafast motions and hydrogen-bonding rearrangements in the active site of a fluorescent protein. However, we demonstrate that the measured motions are not part of the photoisomerization reaction but instead arise from impulsively driven coherent vibrational processes in the electronic ground state. A coherent-control experiment using a two-colour and two-pulse optical excitation strongly amplifies the X-ray crystallographic difference density, while it fully depletes the photoisomerization process. A coherent control mechanism was tested and confirmed the wave packets assignment.

A Unified View on Varied Ultrafast Dynamics of the Primary Process in Microbial Rhodopsins

All-trans to 13-cis photoisomerization of the protonated retinal Schiff base (PRSB) chromophore is the primary step that triggers various biological functions of microbial rhodopsins. While this ultrafast primary process has been extensively studied, it has been recognized that the relevant excited-state relaxation dynamics differ significantly from one rhodopsin to another. To elucidate the origin of the complicated ultrafast dynamics of the primary process in microbial rhodopsins, we studied the excited-state dynamics of proteorhodopsin, its D97N mutant, and bacteriorhodopsin by femtosecond time-resolved absorption (TA) spectroscopy in a wide pH range. The TA data showed that their excited-state relaxation dynamics drastically change when pH approaches the pK_a of the counterion residue of the PRSB chromophore in the ground state. This result reveals that the varied excited-state relaxation dynamics in different rhodopsins mainly originate from the difference of the ground-state heterogeneity (i.e., protonation/deprotonation of the PRSB counterion).

Comparative Femtosecond Spectroscopy of Primary Photoreactions of Exiguobacterium sibiricum Rhodopsin and Halobacterium salinarum Bacteriorhodopsin

The primary stages of the Exiguobacterium sibiricum rhodopsin (ESR) photocycle were investigated by femtosecond absorption laser spectroscopy in the spectral range of 400-900 nm with a time resolution of 25 fs. The dynamics of the ESR photoreaction were compared with the reactions of bacteriorhodopsin (bR) in purple membranes (bR_PM) and in recombinant form (bR_rec). The primary intermediates of the ESR photocycle were similar to intermediates I, J, and K in bacteriorhodopsin photoconversion. The CONTIN program was applied to analyze the characteristic times of the observed processes and to clarify the reaction scheme. A similar photoreaction pattern was observed for all studied retinal proteins, including two consecutive dynamic Stokes shift phases lasting ∼0.05 and ∼0.15 ps. The excited state decays through a femtosecond reactive pathway, leading to retinal isomerization and formation of product J, and a picosecond nonreactive pathway that leads only to the initial state. Retinal photoisomerization in ESR takes 0.69 ps, compared with 0.48 ps in bR_PM and 0.74 ps in bR_rec. The nonreactive excited state decay takes 5 ps in ESR and ∼3 ps in bR. We discuss the similarity of the primary reactions of ESR and other retinal proteins.

Absorption and Emission Spectroscopic Investigation of the Thermal Dynamics of the Archaerhodopsin 3 Based Fluorescent Voltage Sensor QuasAr1

QuasAr1 is a fluorescent voltage sensor derived from Archaerhodopsin 3 (Arch) of Halorubrum sodomense by directed evolution. Here we report absorption and emission spectroscopic studies of QuasAr1 in Tris buffer at pH 8. Absorption cross-section spectra, fluorescence quantum distributions, fluorescence quantum yields, and fluorescence excitation spectra were determined. The thermal stability of QuasAr1 was studied by long-time attenuation coefficient measurements at room temperature (23 ± 2 °C) and at 2.5 ± 0.5 °C. The apparent melting temperature was determined by stepwise sample heating up and cooling down (obtained apparent melting temperature: 65 ± 3 °C). In the protein melting process the originally present protonated retinal Schiff base (PRSB) with absorption maximum at 580 nm converted to de-protonated retinal Schiff base (RSB) with absorption maximum at 380 nm. Long-time storage of QuasAr1 at temperatures around 2.5 °C and around 23 °C caused gradual protonated retinal Schiff base isomer changes to other isomer conformations, de-protonation to retinal Schiff base isomers, and apoprotein structure changes showing up in ultraviolet absorption increase. Reaction coordinate schemes are presented for the thermal protonated retinal Schiff base isomerizations and deprotonations in parallel with the dynamic apoprotein restructurings.

Schiff Base Proton Acceptor Assists Photoisomerization of Retinal Chromophores in Bacteriorhodopsin

In this study, we investigated the ultrafast dynamics of bacteriorhodopsins (BRs) from Haloquadratum walsbyi (HwBR) and Haloarcula marismortui (HmBRI and HmBRII). First, the ultrafast dynamics were studied for three HwBR samples: wild-type, D93N mutation, and D104N mutation. The residues of the D93 and D104 mutants correspond to the control by the Schiff base proton acceptor and donor of the proton translocation subchannels. Measurements indicated that the negative charge from the Schiff base proton acceptor residue D93 interacts with the ultrafast and substantial change of the electrostatic potential associated with chromophore isomerization. By contrast, the Schiff base proton donor assists the restructuring of the chromophore cavity hydrogen-bond network during the thermalization of the vibrational hot state. Second, the ultrafast dynamics of the wild-types of HwBR, HmBRI, and HmBRII were compared. Measurements demonstrated that the hydrogen-bond network in the extracellular region in HwBR and HmBRII slows the photoisomerization of retinal chromophores, and the negatively charged helices on the cytoplasmic side of HwBR and HmBRII accelerate the thermalization of the vibrational hot state of retinal chromophores. The similarity of the correlation spectra of the wild-type HmBRI and D104N mutant of HwBR indicates that inactivation of the Schiff base proton donor induces a positive charge on the helices of the cytoplasmic side.

Painting with Rainbows: Patterning Light in Space, Time, and Wavelength for Multiphoton Optogenetic Sensing and Control

Photons are a fascinating reagent, flowing and reacting quite differently compared to more massive and less ephemeral particles of matter. The optogenetic palette comprises an ever growing set of light-responsive proteins, which open the possibility of using light to perturb and to measure biological processes with great precision in space and time. Yet there are limits on what light can achieve. Diffraction limits the smallest features, and scattering in tissue limits the largest. Photobleaching, diffusion of photogenerated products, and optical crosstalk between overlapping absorption spectra further muddy the optogenetic picture, particularly when one wants to use multiple optogenetic tools simultaneously. But these obstacles are surmountable. Most light-responsive proteins and small molecules undergo more than one light-driven transition, often with different action spectra and kinetics. By overlapping multiple laser beams, carefully patterned in space, time, and wavelength, one can steer molecules into fluorescent or nonfluorescent, active or inactive conformations. By doing so, one can often circumvent the limitations of simple one-photon excitation and achieve new imaging and stimulation capabilities. These include subdiffraction spatial resolution, optical sectioning, robustness to light scattering, and multiplexing of more channels than can be achieved with simple one-photon excitation. The microbial rhodopsins are a particularly rich substrate for this type of multiphoton optical control. The natural diversity of these proteins presents a huge range of starting materials. The spectroscopy and photocycles of microbial rhodopsins are relatively well understood, providing states with absorption maxima across the visible spectrum, which can be accessed on experimentally convenient time scales. A long history of mutational studies in microbial rhodopsins allows semirational protein engineering. Mutants of Archaerhodopsin 3 (Arch) come in all the colors of the rainbow. In a solution of purified Arch-eGFP, a focused green laser excites eGFP fluorescence throughout the laser path, while a focused red laser excites fluorescence of Arch only near the focus, indicative of multiphoton fluorescence. This nonlinearity occurs at a laser intensity ∼10¹⁰-fold lower than in conventional two-photon microscopy! The mutant Arch(D95H) shows photoswitchable optical bistability. In a lawn of E. coli expressing this mutant, illumination with patterned blue light converts the molecule into a state that is fluorescent. Illumination with red light excites this fluorescence, and gradually resets the molecules back to the non-fluorescent state. This review describes the new types of molecular logic that can be implemented with multi-photon control of microbial rhodopsins, from whole-brain activity mapping to measurements of absolute membrane voltage. Part of our goal in this Account is to describe recent work in nonlinear optogenetics, but we also present a variety of interesting things one could do if only the right optogenetic molecules were available. This latter component is intended to inspire future spectroscopic, protein discovery, and protein engineering work.

Empirical rules of molecular photophysics in the light of ultrafast spectroscopy

The advent of ultrafast laser spectroscopy has allowed entirely new possibilities for the investigation of the ultrafast photophysics of inorganic metal-based molecular complexes. In this review we show different regimes where non-Kasha behavior shows up. We also demonstrate that while ultrafast intersystem crossing is a common observation in metal complexes, the ISC rates do not scale with the magnitude of the spin-orbit coupling constant. Structural dynamics and density of states play a crucial role in such ultrafast ISC processes, which are not limited to molecules containing heavy atoms.

Ultrafast photophysics of transition metal complexes

The properties of transition metal complexes are interesting not only for their potential applications in solar energy conversion, OLEDs, molecular electronics, biology, photochemistry, etc. but also for their fascinating photophysical properties that call for a rethinking of fundamental concepts. With the advent of ultrafast spectroscopy over 25 years ago and, more particularly, with improvements in the past 10-15 years, a new area of study was opened that has led to insightful observations of the intramolecular relaxation processes such as internal conversion (IC), intersystem crossing (ISC), and intramolecular vibrational redistribution (IVR). Indeed, ultrafast optical spectroscopic tools, such as fluorescence up-conversion, show that in many cases, intramolecular relaxation processes can be extremely fast and even shorter than time scales of vibrations. In addition, more and more examples are appearing showing that ultrafast ISC rates do not scale with the magnitude of the metal spin-orbit coupling constant, that is, that there is no heavy-atom effect on ultrafast time scales. It appears that the structural dynamics of the system and the density of states play a crucial role therein. While optical spectroscopy delivers an insightful picture of electronic relaxation processes involving valence orbitals, the photophysics of metal complexes involves excitations that may be centered on the metal (called metal-centered or MC) or the ligand (called ligand-centered or LC) or involve a transition from one to the other or vice versa (called MLCT or LMCT). These excitations call for an element-specific probe of the photophysics, which is achieved by X-ray absorption spectroscopy. In this case, transitions from core orbitals to valence orbitals or higher allow probing the electronic structure changes induced by the optical excitation of the valence orbitals, while also delivering information about the geometrical rearrangement of the neighbor atoms around the atom of interest. With the emergence of new instruments such as X-ray free electron lasers (XFELs), it is now possible to perform ultrafast laser pump/X-ray emission probe experiments. In this case, one probes the density of occupied states. These core-level spectroscopies and other emerging ones, such as photoelectron spectroscopy of solutions, are delivering a hitherto unseen degree of detail into the photophysics of metal-based molecular complexes. In this Account, we will give examples of applications of the various methods listed above to address specific photophysical processes.

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.

Mechanism of voltage-sensitive fluorescence in a microbial rhodopsin

Microbial rhodopsins were recently introduced as genetically encoded fluorescent indicators of membrane voltage. An understanding of the mechanism underlying this function would aid in the design of improved voltage indicators. We asked, what states can the protein adopt, and which states are fluorescent? How does membrane voltage affect the photostationary distribution of states? Here, we present a detailed spectroscopic characterization of Archaerhodopsin 3 (Arch). We performed fluorescence spectroscopy on Arch and its photogenerated intermediates in Escherichia coli and in single HEK293 cells under voltage-clamp conditions. These experiments probed the effects of time-dependent illumination and membrane voltage on absorption, fluorescence, membrane current, and membrane capacitance. The fluorescence of Arch arises through a sequential three-photon process. Membrane voltage modulates protonation of the Schiff base in a 13-cis photocycle intermediate (M ⇌ N equilibrium), not in the ground state as previously hypothesized. We present experimental protocols for optimized voltage imaging with Arch, and we discuss strategies for engineering improved rhodopsin-based voltage indicators.

Critical role of Asp227 in the photocycle of proteorhodopsin

The photocycle of the proton acceptor complex mutant D227N of the bacterial retinal protein proteorhodopsin is investigated employing steady state pH-titration experiments in the UV-visible range as well as femtosecond-pump-probe spectroscopy and flash photolysis in the visible spectral range. The evaluation of the pH-dependent spectra showed that the neutralization of the charge at position 227 has a remarkable influence on the ground state properties of the protein. Both the pK(a) values of the primary proton acceptor and of the Schiff base are considerably decreased. Femtosecond-time-resolved measurements demonstrate that the general S(1) deactivation pathway; that is, the K-state formation is preserved in the D227N mutant. However, the pH-dependence of the reaction rate is lost by the substitution of Asp227 with an asparagine. Also no significant kinetic differences are observed upon deuteration. This is explained by the lack of a strongly hydrogen-bonded water in the vicinity of Asp97, Asp227, and the Schiff base or a change in the hydrogen bonding of it (Ikeda et al. (2007) Biochemistry 46, 5365-5373). The flash photolysis measurements prove a considerably elongated photocycle with pronounced pH-dependence. Interestingly, at pH 9 the M-state is visible until the end of the reaction cycle, leading to the conclusion that the mutation does not only lower the pK(a) of the Schiff base in the unphotolyzed ground state but also prevents an efficient reprotonation reaction.

Water-assisted proton transfer in ferredoxin I

The role of water molecules in assisting proton transfer (PT) is investigated for the proton-pumping protein ferredoxin I (FdI) from Azotobacter vinelandii. It was shown previously that individual water molecules can stabilize between Asp(15) and the buried [3Fe-4S](0) cluster and thus can potentially act as a proton relay in transferring H(+) from the protein to the μ(2) sulfur atom. Here, we generalize molecular mechanics with proton transfer to studying proton transfer reactions in the condensed phase. Both umbrella sampling simulations and electronic structure calculations suggest that the PT Asp(15)-COOH + H(2)O + [3Fe-4S](0) → Asp(15)-COO(-) + H(2)O + [3Fe-4S](0) H(+) is concerted, and no stable intermediate hydronium ion (H(3)O(+)) is expected. The free energy difference of 11.7 kcal/mol for the forward reaction is in good agreement with the experimental value (13.3 kcal/mol). For the reverse reaction (Asp(15)-COO(-) + H(2)O + [3Fe-4S](0)H(+) → Asp(15)-COOH + H(2)O + [3Fe-4S](0)), a larger barrier than for the forward reaction is correctly predicted, but it is quantitatively overestimated (23.1 kcal/mol from simulations versus 14.1 from experiment). Possible reasons for this discrepancy are discussed. Compared with the water-assisted process (ΔE ≈ 10 kcal/mol), water-unassisted proton transfer yields a considerably higher barrier of ΔE ≈ 35 kcal/mol.

Confined ultrafast torsional dynamics of Thioflavin-T in a nanocavity

The influence of confinement in the supramolecular β-cyclodextrin nanocavity on the excited state torsional dynamics of the amyloid fibril sensor, Thioflavin-T, is explored using subpicosecond fluorescence up-conversion spectroscopy. In the presence of β-cyclodextrin, the emission intensity and the fluorescence lifetime of Thioflavin-T significantly increases, indicating the confinement effect of the nanocage on the photophysical behaviour of the dye. Detailed time-resolved fluorescence studies show an appreciable dynamic Stokes' shift for the dye in the β-cyclodextrin nanocavity. Analysis of the time-resolved area normalized emission spectra (TRANES) indicates the formation of an emissive TICT state. The rate of formation of the TICT state, as calculated from the time dependent changes in the peak frequency and the width of the emission spectra, is found to be substantially slower in the β-cyclodextrin nanocavity compared to that in bulk water. Present results indicate that ultrafast torsional motion in Thioflavin-T is significantly retarded due to confinement by the β-cyclodextrin nanocavity.

The photocycle of channelrhodopsin-2: ultrafast reaction dynamics and subsequent reaction steps

The photocycle of channelrhodopsin-2 is investigated in a comprehensive study by ultrafast absorption and fluorescence spectroscopy as well as flash photolysis in the visible spectral range. The ultrafast techniques reveal an excited-state decay mechanism analogous to that of the archaeal bacteriorhodopsin and sensory rhodopsin II from Natronomonas pharaonis. After a fast vibrational relaxation of the excited-state population with 150 fs its decay with mainly 400 fs is observed. Hereby, both the initial all-trans retinal ground state and the 13-cis-retinal K photoproduct are populated. The reaction proceeds with a 2.7 ps component assigned to cooling processes. Small spectral shifts are observed on a 200 ps timescale. They are attributed to conformational rearrangements in the retinal binding pocket. The subsequent dynamics progresses with the formation of an M-like intermediate (7 and 120 μs), which decays into red-shifted states within 3 ms. Ground-state recovery including channel closing and reisomerization of the retinal chromophore occurs in a triexponential manner (6 ms, 33 ms, 3.4 s). To learn more about the energy barriers between the different photocycle intermediates, temperature-dependent flash photolysis measurements are performed between 10 and 30°C. The first five time constants decrease with increasing temperature. The calculated thermodynamic parameters indicate that the closing mechanism is controlled by large negative entropy changes. The last time constant is temperature independent, which demonstrates that the photocycle is most likely completed by a series of individual steps recovering the initial structure.

Vibrational fine structures revealed by the frequency-to-time fourier transform of the transient spectrum in bacteriorhodopsin

A vibrational progression that is hidden in a featureless spectrum of induced absorption and stimulated emission was found in time-resolved absorption change spectra. The ultrahigh time resolution of the pump-probe measurement made by using an ultrashort laser pulse localizes the wave packet along the potential multimode hyper surfaces, represented by a vibrational progression. The transition energy of the induced absorption and stimulated emission corresponds to a localized point (space) on the hyper surface, which is visited by the wave packets with fixed phases.

Primary photoinduced protein response in bacteriorhodopsin and sensory rhodopsin II

Essential for the biological function of the light-driven proton pump, bacteriorhodopsin (BR), and the light sensor, sensory rhodopsin II (SRII), is the coupling of the activated retinal chromophore to the hosting protein moiety. In order to explore the dynamics of this process we have performed ultrafast transient mid-infrared spectroscopy on isotopically labeled BR and SRII samples. These include SRII in D(2)O buffer, BR in H(2)(18)O medium, SRII with (15)N-labeled protein, and BR with (13)C(14)(13)C(15)-labeled retinal chromophore. Via observed shifts of infrared difference bands after photoexcitation and their kinetics we provide evidence for nonchromophore bands in the amide I and the amide II region of BR and SRII. A band around 1550 cm(-1) is very likely due to an amide II vibration. In the amide I region, contributions of modes involving exchangeable protons and modes not involving exchangeable protons can be discerned. Observed bands in the amide I region of BR are not due to bending vibrations of protein-bound water molecules. The observed protein bands appear in the amide I region within the system response of ca. 0.3 ps and in the amide II region within 3 ps, and decay partially in both regions on a slower time scale of 9-18 ps. Similar observations have been presented earlier for BR5.12, containing a nonisomerizable chromophore (R. Gross et al. J. Phys. Chem. B 2009, 113, 7851-7860). Thus, the results suggest a common mechanism for ultrafast protein response in the artificial and the native system besides isomerization, which could be induced by initial chromophore polarization.

Primary conformation change in bacteriorhodopsin on photoexcitation

Ultrafast dynamics of bacteriorhodopsin (bR) has been extensively studied experimentally and theoretically. However, there are several contradictory results reported, indicating that its detailed dynamics and initial process have not yet been fully clarified. In this work, changes in the amplitude and phase of molecular vibration in the isomerization process of bR were real-time probed simultaneously at 128 different wavelengths through intensity modulation of the electronic transition. Systematic information on the transient change in continuous spectrum extending from 505 nm (2.45 eV) to 675 nm (1.84 eV) showed different dynamics in each spectral region reflecting the difference in the excited states and intermediates dominating the dynamics during the photoisomerization. Careful analysis of the transient spectral changes and spectrograms calculated from the vibrational real-time traces elucidated that the primary event just after photoexcitation is the deformation of the retinal configuration, which decays within 30 fs near the C=N bond in the protonated Schiff base. The intensity of C=N stretching mode starts to decrease before the initiation of the frequency modulation of the C=C stretching mode. The C=C stretching mode frequency was modulated by a coupled torsion around the C13=C14 bond, leading to the photoisomerization around the bond. This study clarified the dynamics of the C=N and C=C stretching modes working as key vibration modes in the photoisomerization of bR. Furthermore, we have elucidated the modulation and decay dynamics of the C=C stretching mode in the photoreaction starting from H (Franck-Condon excited state) followed by I (twisted excited), and J (first intermediate) states.

Excitation energy-transfer and the relative orientation of retinal and carotenoid in xanthorhodopsin

The cell membrane of Salinibacter ruber contains xanthorhodopsin, a light-driven transmembrane proton pump with two chromophores: a retinal and the carotenoid, salinixanthin. Action spectra for transport had indicated that light absorbed by either is utilized for function. If the carotenoid is an antenna in this protein, its excited state energy has to be transferred to the retinal and should be detected in the retinal fluorescence. From fluorescence studies, we show that energy transfer occurs from the excited singlet S(2) state of salinixanthin to the S(1) state of the retinal. Comparison of the absorption spectrum with the excitation spectrum for retinal emission yields 45 +/- 5% efficiency for the energy transfer. Such high efficiency would require close proximity and favorable geometry for the two polyene chains, but from the heptahelical crystallographic structure of the homologous retinal protein, bacteriorhodopsin, it is not clear where the carotenoid can be located near the retinal. The fluorescence excitation anisotropy spectrum reveals that the angle between their transition dipole moments is 56 +/- 3 degrees . The protein accommodates the carotenoid as a second chromophore in a distinct binding site to harvest light with both extended wavelength and polarization ranges. The results establish xanthorhodopsin as the simplest biological excited-state donor-acceptor system for collecting light.

Coherent oscillations in ultrafast fluorescence of photoactive yellow protein

The ultrafast photoinduced dynamics of photoactive yellow protein in aqueous solution were studied at room temperature by femtosecond fluorescence spectroscopy using an optical Kerr-gate technique. Coherent oscillations of the wave packet were directly observed in the two-dimensional time-energy map of ultrafast fluorescence with 180 fs time resolution and 5 nm spectral resolution. The two-dimensional map revealed that four or more oscillatory components exist within the broad bandwidth of the fluorescence spectrum, each of which is restricted in the respective narrow spectral region. Typical frequencies of the oscillatory modes are 50 and 120 cm(-1). In the landscape on the map, the oscillatory components were recognized as the ridges which were winding and descending with time. The amplitude of the oscillatory and winding behaviors is a few hundred cm(-1), which is the same order as the frequencies of the oscillations. The mean spectral positions of the oscillatory components in the two-dimensional map are well explained by considering the vibrational energies of intramolecular modes in the electronic ground state of the chromophore. The entire view of the wave packet oscillations and broadening in the electronic excited state, accompanied by fluorescence transitions to the vibrational sublevels belonging to the electronic ground state, was obtained.

Sub-5-fs real-time spectroscopy of transition states in bacteriorhodopsin during retinal isomerization

By using a sub-5-fs visible laser pulse, we have made the first observation of the vibrational spectra of the transition state during trans-cis isomerization in the retinal chromophore of bacteriorhodopsin (bR(S68). No instant isomerization of the retinal occurs in spite of electron promotion from the bonding pi-orbital to the anti-bonding pi*-orbital. The difference between the in-plane and out-of-plane vibrational frequencies (about 1150-1250 and 900-1000 cm(-1), respectively) is reduced during the first time period. The vibrational spectra after this period became very broad and weak and are ascribed to a "silent state." The silent state lasts for 700-900 fs until the chromophore isomerizes to the cis-C13 = C14 conformation. The frequency of the C = C stretching mode was modulated by the torsion mode of the C13 = C14 double bond with a period of 200 fs. The modulation was clearly observed for four to five periods. Using the empirical equation for the relation between bond length and stretching frequency, we determined the transitional C = C bond length with about 0.01 angstroms accuracy during the torsion motion around the double bond with 1-fs time resolution.

Femtosecond Stimulated Raman Spectroscopy

Femtosecond stimulated Raman spectroscopy (FSRS) is a new ultrafast spectroscopic technique that provides vibrational structural information with high temporal (50-fs) and spectral (10-cm(1)) resolution. As a result of these unique capabilities, FSRS studies of chemical and biochemical reaction dynamics are expected to grow rapidly, giving previously unattainable insight into the structural dynamics of reactively evolving systems with atomic spatial and femtosecond temporal resolution. This review discusses the experimental and theoretical concepts behind FSRS, with an emphasis on the origins of its unique temporal and spectral capabilities. We illustrate these capabilities with vibrational studies of ultrafast electronic dynamics, as well as the direct structural observation of nonstationary vibrational wave-packet motion in small molecules and in complex biochemical reaction dynamics.

Ultrafast Dynamics of Photoactive Yellow Protein via the Photoexcitation and Emission Processes†

Pump-dump fluorescence spectroscopy was performed for photoactive yellow protein (PYP) at room temperature. The effect of the dump pulse on the population of the potential energy surface of the electronic excited state was examined as depletion in the stationary fluorescence intensity. The dynamic behavior of the population in the electronic excited state was successfully probed in the various combinations of the pump-dump delay, the dump-pulse wavelength, the dump-pulse energy and the observation wavelength. The experimental results were compared with the results obtained by the femtosecond time-resolved fluorescence spectroscopy.

Following Photoinduced Dynamics in Bacteriorhodopsin with 7-fs Impulsive Vibrational Spectroscopy

Sub-10-fs laser pulses are used to impulsively photoexcite bacteriorhodopsin (BR) suspensions and probe the evolution of the resulting vibrational wave packets. Fourier analysis of the spectral modulations induced by transform-limited as well as linearly chirped excitation pulses allows the delineation of excited- and ground-state contributions to the data. On the basis of amplitude and phase variations of the modulations as a function of the dispersed probe wavelength, periodic modulations in absorption above 540 nm are assigned to ground-state vibrational coherences induced by resonance impulsive Raman spectral activity (RISRS). Probing at wavelengths below 540 nm-the red edge of the intense excited-state absorption band-uncovers new vibrational features which are accordingly assigned to wave packet motions along bound coordinates on the short-lived reactive electronic surface. They consist of high- and low-frequency shoulders adjacent to the strong C=C stretching and methyl rock modes, respectively, which have ground-state frequencies of 1008 and 1530 cm-1. Brief activity centered at approximately 900 cm-1, which is characteristic of ground-state HOOP modes, and strong modulations in the torsional frequency range appear as well. Possible assignments of the bands and their implication to photoinduced reaction dynamics in BR are discussed. Reasons for the absence of similar signatures in the pump-probe spectral modulations at longer probing wavelengths are considered as well.

Ultrafast Photoisomerization of Photoactive Yellow Protein Chromophore Analogues in Solution: Influence of the Protonation State

We investigate solvent viscosity and polarity effects on the photoisomerization of the protonated and deprotonated forms of two analogues of the photoactive yellow protein (PYP) chromophore. These are trans-p-hydroxybenzylidene acetone and trans-p-hydroxyphenyl cinnamate, studied in solutions of different polarity and viscosity at room temperature, by means of femtosecond fluorescence up-conversion. The fluorescence lifetimes of the protonated forms are found to be barely sensitive to solvent viscosity, and to increase with increasing solvent polarity. In contrast, the fluorescence decays of the deprotonated forms are significantly slowed down in viscous media and accelerated in polar solvents. These results elucidate the dramatic influence of the protonation state of the PYP chromophore analogues on their photoinduced dynamics. The viscosity and polarity effects are, respectively, interpreted in terms of different isomerization coordinates and charge redistribution in S(1). A trans-to-cis isomerization mechanism involving mainly the ethylenic double-bond torsion and/or solvation is proposed for the anionic forms, whereas "concerted" intramolecular motions are proposed for the neutral forms.

Insights into excited-state and isomerization dynamics of bacteriorhodopsin from ultrafast transient UV absorption

A visible-pump/UV-probe transient absorption is used to characterize the ultrafast dynamics of bacteriorhodopsin with 80-fs time resolution. We identify three spectral components in the 265- to 310-nm region, related to the all-trans retinal, tryptophan (Trp)-86 and the isomerized photoproduct, allowing us to map the dynamics from reactants to products, along with the response of Trp amino acids. The signal of the photoproduct appears with a time delay of approximately 250 fs and is characterized by a steep rise ( approximately 150 fs), followed by additional rise and decay components, with time scales characteristic of the J intermediate. The delayed onset and the steep rise point to an impulsive formation of a transition state on the way to isomerization. We argue that this impulsive formation results from a splitting of a wave packet of torsional modes on the potential surface at the branching between the all-trans and the cis forms. Parallel to these dynamics, the signal caused by Trp response rises in approximately 200 fs, because of the translocation of charge along the conjugate chain, and possible mechanisms are presented, which trigger isomerization.

Twisting Dynamics in the Excited Singlet State of Michler's Ketone

Ultrafast relaxation dynamics of the excited singlet (S(1)) state of Michler's ketone (MK) has been investigated in different kinds of solvents using a time-resolved absorption spectroscopic technique with 120 fs time resolution. This technique reveals that conversion of the locally excited (LE) state to the twisted intramolecular charge transfer (TICT) state because of twisting of the N,N-dimethylanilino groups with respect to the central carbonyl group is the major relaxation process responsible for the multi-exponential and probe-wavelength-dependent transient absorption dynamics of the S1 state of MK, but solvation dynamics does not have a significant role in this process. Theoretical optimization of the ground-state geometry of MK shows that the dimethylanilino groups attached to the central carbonyl group are at a dihedral angle of about 51 degrees with respect to each other because of steric interaction between the phenyl rings. Following photoexcitation of MK to its S1 state, two kinds of twisting motions have been resolved. Immediately after photoexcitation, an ultrafast "anti-twisting" motion of the dimethylanilino groups brings back the pretwisted molecule to a near-planar geometry with high mesomeric interaction and intramolecular charge transfer (ICT) character. This motion is observed in all kinds of solvents. Additionally, in solvents of large polarity, the dimethylamino groups undergo further twisting to about 90 degrees with respect to the phenyl ring, to which it is attached, leading to the conversion of the ICT state to the TICT state. Similar characteristics of the absorption spectra of the TICT state and the anion radical of MK establish the nearly pure electron transfer (ET) character of the TICT state. In aprotic solvents, because of the steep slope of the potential energy surface near the Franck-Condon (FC) or LE state region, the LE state is nearly nonemissive at room temperature and fluorescence emission is observed from only the ICT and TICT states. Alternatively, in protic solvents, because of an intermolecular hydrogen-bonding interaction between MK and the solvent, the LE region is more flat and stimulated emission from this state is also observed. However, a stronger hydrogen-bonding interaction between the TICT state and the solvent as well as the closeness between the two potential energy surfaces due to the TICT and the ground states cause the nonradiative coupling between these states to be very effective and, hence, cause the TICT state to be weakly emissive. The multi-exponentiality and strong wavelength-dependence of the kinetics of the relaxation process taking place in the S1 state of MK have arisen for several reasons, such as strong overlapping of transient absorption and stimulated emission spectra of the LE, ICT, and TICT states, which are formed consecutively following photoexcitation of the molecule, as well as the fact that different probe wavelengths monitor different regions of the potential energy surface representing the twisting motion of the excited molecule.