Real-time spectroscopy of transition states in bacteriorhodopsin during retinal isomerization

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.

Four-wave mixing signals from beta-carotene and its n = 15 homologue

The third-order nonlinear optical responses of beta-carotene and its homologue having a conjugation-double bond n = 15 have been investigated using sub-20 fs ultra-short optical pulses in order to clarify the dissipation processes of excess energy. Using the four-wave mixing spectroscopy, we observed a clear coherent oscillation with a period of a few tens of femtoseconds. The spectral density of these molecules was estimated that allowed the theoretical linear and nonlinear optical signals to be directly compared with the experimental data. Calculations based on the Brownian oscillator model were performed under the impulsive excitation limit. We show that the memory of the vibronic coherence generated upon the excitation into the S(2) state is lost via the relaxation process including the S(1) state. The vibronic decoherence lifetime of the system was estimated to be 1 ps, which is about 5 times larger than the life time of the S(2) state ( approximately 150 fs) determined in previous studies. The role of coherence and the efficient energy transfer in the light-harvesting antenna complexes are discussed.

Simple, efficient, and modular syntheses of polyene natural products via iterative cross-coupling

This communication describes the discovery of air-stable and highly versatile B-protected haloalkenylboronic acid building blocks for iterative cross-coupling. These reagents enable the total synthesis of polyene natural products with extraordinary levels of simplicity, efficiency, and modularity. Specifically, all-trans -retinal, β-parinaric acid, and one-half the amphotericin B macrolide skeleton were prepared using only the Suzuki-Miyaura reaction in an iterative manner to bring together collections of simple and readily-accessible building blocks. In contrast to their boronic acid counterparts, the intermediate polyenylboronate esters are remarkably stable (to both column purification and storage), which is critical to their successful utilization. Moreover, the reactive boronic acids can be cleanly liberated using very mild aqueous base. These advances have enabled preparation of the longest polyene ever synthesized using the SM reaction. We additionally report, to the best of our knowledge, the first triply metal selective (Zn vs. Sn and B) cross-coupling reaction, the first selective cross-coupling with a differentially-ligated diboron reagent, and the first cross-couplings between polyenylchlorides and vinylboronic acids. Collectively, these new building blocks and methods can dramatically improve the way polyene natural products and their derivatives are synthesized in the laboratory.

Classification of dynamic vibronic couplings in vibrational real-time spectra of a thiophene derivative by few-cycle pulses

Pump-probe spectroscopy was performed with a few cycle pulses of 6.7 fs duration. The electronic transition intensity modulation was induced by molecular vibration in a quinoid thiophene molecule in solution. The real-time vibrational features were analyzed in terms of dependence of vibrational amplitude and phase on probe photon energy. The electronic transition probability is modulated by molecular vibration via vibronic coupling. Changes in the spectral shape and intensity of the time-resolved spectrum were studied by tracking characteristic spectral features including the peak frequency and intensity, spectral bandwidth, and band-integrated intensity. From the analysis the modulation mechanisms were classified into two groups: (1) Condon type and (2) non-Condon type. The features of the wave packet motions were also classified into zeroth-order derivatives due to quasi-pure non-Condon type and first- and second-order derivative types due to the displacement of the potential minimum and the potential curvature change associated with the relevant vibronic transition, respectively.

High-time-resolution pump-probe system with broadband detection for the study of time-domain vibrational dynamics

We present an ultrafast transient absorption spectroscopy system in the visible combining high-sensitivity broadband detection with extreme temporal resolution. The instrument is based on an ultrabroadband sub-10 fs optical parametric amplifier coupled to an optical multichannel analyzer with fast electronics, enabling single-shot detection at 1 kHz repetition rate. For a given pump-probe delay tau, we achieve a differential transmission (DeltaTT) sensitivity of the order of 10(-4) over the lambda(pr)=490-720 nm probe wavelength range by averaging over 1000 shots, allowing the acquisition of complete two-dimensional DeltaTT (lambda(pr),Tau) maps within a few minute measurement time. We present application examples highlighting the capability of this instrument to observe ultrafast dynamical processes, follow impulsively excited vibrational motions with frequency as high as 3000 cm(-1) (11 fs period), and determine the probe wavelength dependence of amplitude and phase of the oscillations.

Subpicosecond protein backbone changes detected during the green-absorbing proteorhodopsin primary photoreaction

Recent studies demonstrate that photoactive proteins can react within several picoseconds to photon absorption by their chromophores. Faster subpicosecond protein responses have been suggested to occur in rhodopsin-like proteins where retinal photoisomerization may impulsively drive structural changes in nearby protein groups. Here, we test this possibility by investigating the earliest protein structural changes occurring in proteorhodopsin (PR) using ultrafast transient infrared (TIR) spectroscopy with approximately 200 fs time resolution combined with nonperturbing isotope labeling. PR is a recently discovered microbial rhodopsin similar to bacteriorhodopsin (BR) found in marine proteobacteria and functions as a proton pump. Vibrational bands in the retinal fingerprint (1175-1215 cm(-1)) and ethylenic stretching (1500-1570 cm(-1)) regions characteristic of all-trans to 13-cis chromophore isomerization and formation of a red-shifted photointermediate appear with a 500-700 fs time constant after photoexcitation. Bands characteristic of partial return to the ground state evolve with a 2.0-3.5 ps time constant. In addition, a negative band appears at 1548 cm(-1) with a time constant of 500-700 fs, which on the basis of total-15N and retinal C15D (retinal with a deuterium on carbon 15) isotope labeling is assigned to an amide II peptide backbone mode that shifts to near 1538 cm(-1) concomitantly with chromophore isomerization. Our results demonstrate that one or more peptide backbone groups in PR respond with a time constant of 500-700 fs, almost coincident with the light-driven retinylidene chromophore isomerization. The protein changes we observe on a subpicosecond time scale may be involved in storage of the absorbed photon energy subsequently utilized for proton transport.

Stairway to the conical intersection: a computational study of the retinal isomerization

The potential-energy surface of the first excited state of the 11-cis-retinal protonated Schiff base (PSB11) chromophore has been studied at the density functional theory (DFT) level using the time-dependent perturbation theory approach (TDDFT) in combination with Becke's three-parameter hybrid functional (B3LYP). The potential-energy curves for torsion motions around single and double bonds of the first excited state have also been studied at the coupled-cluster approximate singles and doubles (CC2) level. The corresponding potential-energy curves for the ground state have been calculated at the B3LYP DFT and second-order Møller-Plesset (MP2) levels. The TDDFT study suggests that the electronic excitation initiates a turn of the beta-ionone ring around the C6-C7 bond. The torsion is propagating along the retinyl chain toward the cis to trans isomerization center at the C11=C12 double bond. The torsion twist of the C10-C11 single bond leads to a significant reduction in the deexcitation energy indicating that a conical intersection is being reached by an almost barrierless rotation around the C10-C11 single bond. The energy released when passing the conical intersection can assist the subsequent cis to trans isomerization of the C11=C12 double bond. The CC2 calculations also show that the torsion barrier for the twist of the retinyl C10-C11 single bond adjacent to the isomerization center almost vanishes for the excited state. Because of the reduced torsion barriers of the single bonds, the retinyl chain can easily deform in the excited state. Thus, the CC2 and TDDFT calculations suggest similar reaction pathways on the potential-energy surface of the excited state leading toward the conical intersection and resulting in a cis to trans isomerization of the retinal chromophore. According to the CC2 calculations the cis to trans isomerization mechanism does not involve any significant torsion motion of the beta-ionone ring.

Imaging the dynamic behaviour of individual retinal chromophores confined inside carbon nanotubes

Retinal is the molecule found in photoreceptor cells that undergoes a change in shape when it absorbs light. Specifically, the cis/trans isomerization of a carbon-carbon double bond in this chromophore sets in motion the chain of biochemical processes responsible for vision. Here, we obtain atomically resolved images of individual structural isomers of the retinal chromophore attached to C60 molecules and study their dynamic behaviour inside a confined space--that is, inside single-walled carbon nanotubes--using high-resolution transmission electron microscopy (HR-TEM). Sequential HR-TEM images with sub-second time resolution directly reveal the isomerization between the cis and all-trans forms of retinal, as well as conformational changes and volume-conserving effects. This work opens up the possibility of investigating in vitro the biological activities of these photoresponsive molecules on an individual basis, and the molecular imaging technique described here is a general one that can be applied to a wide range of systems.

Determination of the Formation of Dark State via Depleted Spontaneous Emission in a Complex Solvated Molecule

We present a general two-color two-pulse femtosecond pump-dump approach to study the specific population transfer along the reaction coordinate through the higher vibrational energy levels of excited states of a complex solvated molecule via the depleted spontaneous emission. The time-dependent fluorescence depletion provides the correlated dynamical information between the monitored fluorescence state and the SEP "dumped" dark states, and therefore allow us to obtain the dynamics of the formation of the dark states corresponding to the ultrafast photoisomerization processes. The excited-state dynamics of LDS 751 have been investigated as a function of solvent viscosity and solvent polarity, where a cooperative two-step isomerization process is clearly identified within LDS 751 upon excitation.

Inter-helical Hydrogen Bonds Are Essential Elements for Intra-protein Signal Transduction: The Role of Asp115 in Bacteriorhodopsin Transport Function

The behavior of the D115A mutant was analyzed by time-resolved UV-Vis and Fourier transformed infrared (FTIR) spectroscopies, aiming to clarify the role of Asp115 in the intra-protein signal transductions occurring during the bacteriorhodopsin photocycle. UV-Vis data on the D115A mutant show severely desynchronized photocycle kinetics. FTIR data show a poor transmission of the retinal isomerization to the chromoprotein, evidenced by strongly attenuated helical changes (amide I), the remarkable absence of environment alterations and protonation/deprotonation events related to Asp96 and direct Schiff base (SB) protonation form the bulk. This argues for the interactions of Asp115 with Leu87 (via water molecule) and Thr90 as key elements for the effective and vectorial proton path between Asp96 and the SB, in the cytoplasmic half of bacteriorhodopsin. The results strongly suggest the presence of a regulation motif enclosed in helices C and D (Thr90-Pro91/Asp115) which drives properly the dynamics of helix C through a set of interactions. It also supports the idea that intra-helical hydrogen bonding clusters in the buried regions of transmembrane proteins can be potential elements in intra-protein signal transduction.

Observation of terahertz vibrations in Pyrococcus furiosus rubredoxin via impulsive coherent vibrational spectroscopy and nuclear resonance vibrational spectroscopy – interpretation by molecular mechanics

We have used impulsive coherent vibrational spectroscopy (ICVS) to study the Fe(S-Cys)(4) site in oxidized rubredoxin (Rd) from Pyrococcus furiosus (Pf). In this experiment, a 15 fs visible laser pulse is used to coherently pump the sample to an excited electronic state, and a second <10 fs pulse is used to probe the change in transmission as a function of the time delay. PfRd was observed to relax to the ground state by a single exponential decay with time constants of approximately 255-275 fs. Superimposed on this relaxation are oscillations caused by coherent excitation of vibrational modes in both excited and ground electronic states. Fourier transformation reveals the frequencies of these modes. The strongest ICV mode with 570 nm excitation is the symmetric Fe-S stretching mode near 310 cm(-1), compared to 313 cm(-1) in the low temperature resonance Raman. If the rubredoxin is pumped at 520 nm, a set of strong bands occurs between 20 and 110 cm(-1). Finally, there is a mode at approximately 500 cm(-1) which is similar to features near 508 cm(-1) in blue Cu proteins that have been attributed to excited state vibrations. Normal mode analysis using 488 protein atoms and 558 waters gave calculated spectra that are in good agreement with previous nuclear resonance vibrational spectra (NRVS) results. The lowest frequency normal modes are identified as collective motions of the entire protein or large segments of polypeptide. Motion in these modes may affect the polar environment of the redox site and thus tune the electron transfer functions in rubredoxins.

Femtosecond quantum control of molecular dynamics in the condensed phase

We review the progress in controlling quantum dynamical processes in the condensed phase with femtosecond laser pulses. Due to its high particle density the condensed phase has both high relevance and appeal for chemical synthesis. Thus, in recent years different methods have been developed to manipulate the dynamics of condensed-phase systems by changing one or multiple laser pulse parameters. Single-parameter control is often achieved by variation of the excitation pulse's wavelength, its linear chirp or its temporal subpulse separation in case of pulse sequences. Multiparameter control schemes are more flexible and provide a much larger parameter space for an optimal solution. This is realized in adaptive femtosecond quantum control, in which the optimal solution is iteratively obtained through the combination of an experimental feedback signal and an automated learning algorithm. Several experiments are presented that illustrate the different control concepts and highlight their broad applicability. These fascinating achievements show the continuous progress on the way towards the control of complex quantum reactions in the condensed phase.

Time-resolved methods in biophysics. 4. Broadband pump–probe spectroscopy system with sub-20 fs temporal resolution for the study of energy transfer processes in photosynthesis

In this paper we discuss how to push the temporal resolution limits of transient absorption spectroscopy in order to detect very fast processes (energy relaxation, energy or charge transfer, vibrational coherence) taking place in molecules of biological relevance. After reviewing the main principles of femtosecond pump-probe spectroscopy, we describe an experimental setup based on two synchronized non-collinear optical parametric amplifiers (NOPAs). Each NOPA can be independently configured to generate ultra-broadband sub-10 fs visible pulses, tunable 10-15 fs visible pulses, tunable 15-40 fs near-infrared pulses (900-1500 nm). This system enables to perform pump-probe experiments over nearly two octaves of spectrum with sub-20 fs temporal resolution. We then present an application example highlighting the capability of this instrument to track excited state dynamics in biomolecules on the sub-100 fs timescale: the study of carotenoid-bacteriochlorophyll energy transfer processes in peripheral light-harvesting complexes (LH2) from purple bacteria. We show that, by comparing excited-state dynamics of the carotenoids in organic solvents and inside the LH2 complexes, it is possible to visualize in the time domain the primary events in photosynthesis.

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.

Coherent control of retinal isomerization in bacteriorhodopsin

Optical control of the primary step of photoisomerization of the retinal molecule in bacteriorhodopsin from the all-trans to the 13-cis state was demonstrated under weak field conditions (where only 1 of 300 retinal molecules absorbs a photon during the excitation cycle) that are relevant to understanding biological processes. By modulating the phases and amplitudes of the spectral components in the photoexcitation pulse, we showed that the absolute quantity of 13-cis retinal formed upon excitation can be enhanced or suppressed by +/-20% of the yield observed using a short transform-limited pulse having the same actinic energy. The shaped pulses were shown to be phase-sensitive at intensities too low to access different higher electronic states, and so these pulses apparently steer the isomerization through constructive and destructive interference effects, a mechanism supported by observed signatures of vibrational coherence. These results show that the wave properties of matter can be observed and even manipulated in a system as large and complex as a protein.

Real-time propagation time-dependent density functional theory study on the ring-opening transformation of the photoexcited crystalline benzene

Mechanism of the ring-opening transformation in the photoexcited crystalline benzene is investigated on the femtosecond scale by a computational method based on the real-time propagation (RTP) time-dependent density functional theory (TDDFT). The excited-state dynamics of the benzene molecule is also examined not only for the distinction between the intrinsic properties of molecule and the intermolecular interaction but for the first validation using the vibration frequencies for the RTP-TDDFT approach. It is found that the vibration frequencies of the excited and ground states in the molecule are well reproduced. This demonstrates that the present method of time evolution using the Suzuki-Trotter-type split operator technique starting with the Franck-Condon state approximated by the occupation change of the Kohn-Sham orbitals is adequately accurate. For the crystalline benzene, we carried out the RTP-TDDFT simulations for two typical pressures. At both pressures, large swing of the C-H bonds and subsequent twist of the carbon ring occurs, leading to tetrahedral (sp3-like) C-H bonding. The nu4 and nu16 out-of-plane vibration modes of the benzene molecule are found mostly responsible for these motions, which is different from the mechanism proposed for the thermal ring-opening transformation occurring at higher pressure. Comparing the results between different pressures, we conclude that a certain increase of the intermolecular interaction is necessary to make seeds of the ring opening (e.g., radical site formation and breaking of the molecular character) even with the photoexcitation, while the hydrogen migration to fix them requires more free volume, which is consistent with the experimental observation that the transformation substantially proceeds on the decompression.

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.

Probing the ultrafast charge translocation of photoexcited retinal in bacteriorhodopsin

The ultrafast evolution of the electric field within bacteriorhodopsin was measured by monitoring the absorption changes of a tryptophan residue after excitation of retinal. The Trp absorption decreases within the first 200 femtoseconds and then recovers on time scales typical for retinal isomerization and vibrational relaxation. A model of excitonic coupling between retinal and tryptophans shows that the signal reflects a gradual rise of the retinal difference dipole moment, which precedes and probably drives isomerization. The results suggest an intimate connection between the progressive dipole moment change and the retinal skeletal changes reported over the same time scale.

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.

Enhancement and Suppression of Vibrational Coherence in Degenerate Four-Wave-Mixing Signal Generated from Dye-Doped Polymer Films

Vibrational coherence in the degenerate four-wave-mixing (DFWM) signal generated from polymer films doped with a dye, oxazine 4 (Ox4), at 10 K was investigated. It was found that the amplitudes of some low-frequency oscillations (<400 cm(-1)) were enhanced when the delay between the first and second femtosecond pulses was set out of phase with the oscillation period. Frequency and reorganization energy dependence was investigated by computer simulation based on the response function formalism which considers all the possible Liouville space pathways for the DFWM signal. It was revealed that low-frequency oscillations with weak coupling to the optical transition can be enhanced in the stimulated photon echo signal compared to the transient grating signal.

Real-Time Charge Oscillation between Monomers in a Dimeric System Associated with Intermolecular Vibration Induced by an Ultrashort Pulse

Ultrafast charge resonant (CR) dynamics between two molecules in a dimer system has been studied theoretically and experimentally using 6-fs laser pulses and a thin film of amorphous-phase phthalocyanine tin(IV) dichloride (SnPc). The modulation of the absorbance change in the bleaching spectral range of the CR absorption band was analyzed to obtain the amount of charge resonantly transferred back and forth by a dimeric vibration induced by photoexcitation. The modulation can be explained in terms of a periodic change in the cross section and a periodic energy shift, where both are induced by the change in the overlap integral caused by the accordion-type intermolecular vibration. The associated change in distance between two molecules with the intermolecular vibration was estimated to be 0.09 A, which corresponds to 2.5% of the mean distance between the two SnPc molecules in the dimeric system.

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.