Control of retinal isomerization in bacteriorhodopsin in the high-intensity regime

Resonant multiphoton processes and excitation limits to structural dynamics

Understanding the chemical reactions that give rise to functional biological systems is at the core of structural biology. As techniques are developed to study the chemical reactions that drive biological processes, it must be ensured that the reaction occurring is indeed a biologically relevant pathway. There is mounting evidence indicating that there has been a propagation of systematic error in the study of photoactive biological processes; the optical methods used to probe the structural dynamics of light activated protein functions have failed to ensure that the photoexcitation prepares a well-defined initial state relevant to the biological process of interest. Photoexcitation in nature occurs in the linear (one-photon per chromophore) regime; however, the extreme excitation conditions used experimentally give rise to biologically irrelevant multiphoton absorption. To evaluate and ensure the biological relevance of past and future experiments, a theoretical framework has been developed to determine the excitation conditions, which lead to resonant multiphoton absorption (RMPA) and thus define the excitation limit in general for the study of structural dynamics within the 1-photon excitation regime. Here, we apply the theoretical model to bacteriorhodopsin (bR) and show that RMPA occurs when excitation conditions exceed the linear saturation threshold, well below typical excitation conditions used in this class of experiments. This work provides the guidelines to ensure excitation in the linear 1-photon regime is relevant to biological and chemical processes.

Optical Control of Crossing the Conical Intersection in β-Carotene

Optical control of dynamic processes has been challenging yet has only been demonstrated in several chemical and biological systems. The control of a reaction passing the widely present conical intersection has not been realized. Here, we modulated the phase of the excitation pulse to control the dynamics of β-carotene through accessing the conical intersection (CI). We observed different dynamics in 110-220 fs into the CI and the consecutive process in 400-600 fs through another CI by various chirped excitation pulses. We successfully controlled those ultrafast wavepacket dynamics passing the CIs on the femtosecond time scales. The method developed here can be used to control a various of ultrafast chemical and biological reactions through the CI(s).

Voltage Imaging with Engineered Proton-Pumping Rhodopsins: Insights from the Proton Transfer Pathway

Voltage imaging using genetically encoded voltage indicators (GEVIs) has taken the field of neuroscience by storm in the past decade. Its ability to create subcellular and network level readouts of electrical dynamics depends critically on the kinetics of the response to voltage of the indicator used. Engineered microbial rhodopsins form a GEVI subclass known for their high voltage sensitivity and fast response kinetics. Here we review the essential aspects of microbial rhodopsin photocycles that are critical to understanding the mechanisms of voltage sensitivity in these proteins and link them to insights from efforts to create faster, brighter and more sensitive microbial rhodopsin-based GEVIs.

Serial Femtosecond Crystallography Reveals that Photoactivation in a Fluorescent Protein Proceeds via the Hula Twist Mechanism

Chromophore cis/trans photoisomerization is a fundamental process in chemistry and in the activation of many photosensitive proteins. A major task is understanding the effect of the protein environment on the efficiency and direction of this reaction compared to what is observed in the gas and solution phases. In this study, we set out to visualize the hula twist (HT) mechanism in a fluorescent protein, which is hypothesized to be the preferred mechanism in a spatially constrained binding pocket. We use a chlorine substituent to break the twofold symmetry of the embedded phenolic group of the chromophore and unambiguously identify the HT primary photoproduct. Through serial femtosecond crystallography, we then track the photoreaction from femtoseconds to the microsecond regime. We observe signals for the photoisomerization of the chromophore as early as 300 fs, obtaining the first experimental structural evidence of the HT mechanism in a protein on its femtosecond-to-picosecond timescale. We are then able to follow how chromophore isomerization and twisting lead to secondary structure rearrangements of the protein β-barrel across the time window of our measurements.

Nonadiabatic Excited State Dynamics of Organic Chromophores: Take-Home Messages

Nonadiabatic excited state dynamics are important in a variety of processes. Theoretical and experimental developments have allowed for a great progress in this area, while combining the two is often necessary and the best approach to obtain insight into the photophysical behavior of molecules. In this Feature Article we use examples of our recent work combining time-resolved photoelectron spectroscopy with theoretical nonadiabatic dynamics to highlight important lessons we learned. We compare the nonadiabatic excited state dynamics of three different organic molecules with the aim of elucidating connections between structure and dynamics. Calculations and measurements are compared for uracil, 1,3-cyclooctadiene, and 1,3-cyclohexadiene. The comparison highlights the role of rigidity in influencing the dynamics and the difficulty of capturing the dynamics accurately with calculations.

Ultrafast pulse shaping modulates perceived visual brightness in living animals

Vision is usually assumed to be sensitive to the light intensity and spectrum but not to its spectral phase. However, experiments performed on retinal proteins in solution showed that the first step of vision consists in an ultrafast photoisomerization that can be coherently controlled by shaping the phase of femtosecond laser pulses, especially in the multiphoton interaction regime. The link between these experiments in solution and the biological process allowing vision was not demonstrated. Here, we measure the electric signals fired from the retina of living mice upon femtosecond multipulse and single-pulse light stimulation. Our results show that the electrophysiological signaling is sensitive to the manipulation of the light excitation on a femtosecond time scale. The mechanism relies on multiple interactions with the light pulses close to the conical intersection, like pump-dump (photoisomerization interruption) and pump-repump (reverse isomerization) processes. This interpretation is supported both experimentally and by dynamics simulations.

Excited state dynamics of cis,cis-1,3-cyclooctadiene: UV pump VUV probe time-resolved photoelectron spectroscopy

We present UV pump, vacuum ultraviolet probe time-resolved photoelectron spectroscopy measurements of the excited state dynamics of cis,cis-1,3-cyclooctadiene. A 4.75 eV deep UV pump pulse launches a vibrational wave packet on the first electronically excited state, and the ensuing dynamics are probed via ionization using a 7.92 eV probe pulse. The experimental results indicate that the wave packet undergoes rapid internal conversion to the ground state in under 100 fs. Comparing the measurements with electronic structure and trajectory surface hopping calculations, we are able to interpret the features in the measured photoelectron spectra in terms of ionization to several states of the molecular cation.

Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin

Bacteriorhodopsin (bR) is a light-driven proton pump. The primary photochemical event upon light absorption is isomerization of the retinal chromophore. Here we used time-resolved crystallography at an X-ray free-electron laser to follow the structural changes in multiphoton-excited bR from 250 femtoseconds to 10 picoseconds. Quantum chemistry and ultrafast spectroscopy were used to identify a sequential two-photon absorption process, leading to excitation of a tryptophan residue flanking the retinal chromophore, as a first manifestation of multiphoton effects. We resolve distinct stages in the structural dynamics of the all-trans retinal in photoexcited bR to a highly twisted 13-cis conformation. Other active site sub-picosecond rearrangements include correlated vibrational motions of the electronically excited retinal chromophore, the surrounding amino acids and water molecules as well as their hydrogen bonding network. These results show that this extended photo-active network forms an electronically and vibrationally coupled system in bR, and most likely in all retinal proteins.

Bacteriorhodopsin (bR) is a light-driven proton pump. Here the authors combine time-resolved crystallography at a free-electron laser, ultrafast spectroscopy and quantum chemistry to study the structural changes following multiphoton photoexcitation of bR and find that they occur within 300 fs not only in the light-absorbing chromophore but also in the surrounding protein.

Bacteriorhodopsin: Structural Insights Revealed Using X-Ray Lasers and Synchrotron Radiation

Directional transport of protons across an energy transducing membrane—proton pumping—is ubiquitous in biology. Bacteriorhodopsin (bR) is a light-driven proton pump that is activated by a buried all- trans retinal chromophore being photoisomerized to a 13- cis conformation. The mechanism by which photoisomerization initiates directional proton transport against a proton concentration gradient has been studied by a myriad of biochemical, biophysical, and structural techniques. X-ray free electron lasers (XFELs) have created new opportunities to probe the structural dynamics of bR at room temperature on timescales from femtoseconds to milliseconds using time-resolved serial femtosecond crystallography (TR-SFX). Wereview these recent developments and highlight where XFEL studies reveal new details concerning the structural mechanism of retinal photoisomerization and proton pumping. We also discuss the extent to which these insights were anticipated by earlier intermediate trapping studies using synchrotron radiation. TR-SFX will open up the field for dynamical studies of other proteins that are not naturally light-sensitive.

Stepwise Two-Photon-Induced Electron Transfer from Higher Excited States of Noncovalently Bound Porphyrin-CdS/ZnS Core/Shell Nanocrystals

There has been an increasing amount of interest in stepwise two-photon-absorption (2PA)-induced photochemical reactions because of their extremely lower power thresholds compared to that of the simultaneous process and drastic reaction enhancements in some cases. However, stepwise 2PA-induced photochemical reactions were reported only in single chromophores and covalently bound bichromophores and there are few reports on these reactions in noncovalently bound systems because of weak electronic interactions among chromophores. This study demonstrated the stepwise 2PA-induced electron transfer from higher excited states in noncovalently bound protoporphyrin IX·CdS/ZnS core/shell nanocrystals (NCs). The electron transfer from higher excited states of porphyrin to CdS NCs successfully overcomes the activation barrier associated with the wide bandgap ZnS shell, indicating that a high reduction potential can be obtained with the stepwise 2PA process. The concept presented in this study can be applied to various noncovalently bound multichromophore systems to explore nonlinear photoresponses.

Multiphoton-gated cycloreversion reaction of a fluorescent diarylethene derivative as revealed by transient absorption spectroscopy

The one- and two-photon cycloreversion reactions of a fluorescent diarylethene derivative with oxidized benzothiophene moieties were investigated by means of ultrafast laser spectroscopy. Femtosecond transient absorption spectroscopy under the one-photon excitation condition revealed that the excited closed-ring isomer is simply deactivated into the initial ground state with a time constant of 2.6 ns without remarkable cycloreversion, the results of which are consistent with the very low cycloreversion reaction yield (<10-5) under steady-state light irradiation. On the other hand, an efficient cycloreversion reaction was observed under irradiation with a picosecond laser pulse at 532 nm. The excitation intensity dependence of the cycloreversion reaction indicates that a highly excited state attained by the stepwise two-photon absorption is responsible for the marked increase of the cycloreversion reaction, and the quantum yield at the highly excited state was estimated to be 0.018 from quantitative analysis, indicating that the reaction is enhanced by a factor of >1800.

Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser

Ultrafast isomerization of retinal is the primary step in photoresponsive biological functions including vision in humans and ion transport across bacterial membranes. We used an x-ray laser to study the subpicosecond structural dynamics of retinal isomerization in the light-driven proton pump bacteriorhodopsin. A series of structural snapshots with near-atomic spatial resolution and temporal resolution in the femtosecond regime show how the excited all-trans retinal samples conformational states within the protein binding pocket before passing through a twisted geometry and emerging in the 13-cis conformation. Our findings suggest ultrafast collective motions of aspartic acid residues and functional water molecules in the proximity of the retinal Schiff base as a key facet of this stereoselective and efficient photochemical reaction.

Efficient Cycloreversion Reaction of a Diarylethene Derivative in Higher Excited States Attained by Off-Resonant Simultaneous Two-Photon Absorption

Off-resonant excitation of the closed-ring isomer of a photochromic diarylethene derivative at 730 nm induced the efficient cycloreversion reaction with a yield of ∼20%, while the reaction yield was only 2% under one-photon excitation at 365 nm. Excitation wavelength dependence of the one-photon cycloreversion reaction yield under steady-state irradiation in a wide wavelength range showed that the specific electronic state leading to the large cycloreversion reaction yield, which is originally forbidden in the optical transition but partially allowed owing to the low symmetry of the molecule, is spectrally overlapped with the electronic state accessible by the allowed one-photon optical transition in the UV region. Femtosecond transient absorption spectroscopy also revealed that the off-resonant two-photon excitation preferentially pumped the molecule into the specific state, leading to the 10-fold enhancement of the cycloreversion reaction.

Phase-Modulated Nonresonant Laser Pulses Can Selectively Convert Enantiomers in a Racemic Mixture

Deracemization occurs when a racemic molecular mixture is transformed into a mixture containing an excess of a single enantiomer. Recent advances in ultrafast laser technology hint at the possibility of using shaped pulses to generate deracemization via selective enantiomeric conversion; however, experimental implementation remains a challenge and has not yet been achieved. Here we suggest a simple, yet novel approach to laser-induced enantiomeric conversion based on dynamic Stark control. We demonstrate theoretically that current laser and optical technology can be used to generate a pair of phase-modulated, nonresonant, linearly polarized Gaussian laser pulses that can selectively deracemize a racemic mixture of 3D-oriented, 3,5-difluoro-3',5'-dibromobiphenyl (F₂H₃C₆-C₆H₃Br₂) molecules, the laser-induced dynamics of which are well studied experimentally. These results strongly suggest that designing a closed-loop coherent control scheme based on this methodology may lead to the first-ever achievement of enantiomeric conversion via coherent laser light in a laboratory setting.

Non-resonant dynamic stark control of vibrational motion with optimized laser pulses

The term dynamic Stark control (DSC) has been used to describe methods of quantum control related to the dynamic Stark effect, i.e., a time-dependent distortion of energy levels. Here, we employ analytical models that present clear and concise interpretations of the principles behind DSC. Within a linearly forced harmonic oscillator model of vibrational excitation, we show how the vibrational amplitude is related to the pulse envelope, and independent of the carrier frequency of the laser pulse, in the DSC regime. Furthermore, we shed light on the DSC regarding the construction of optimal pulse envelopes - from a time-domain as well as a frequency-domain perspective. Finally, in a numerical study beyond the linearly forced harmonic oscillator model, we show that a pulse envelope can be constructed such that a vibrational excitation into a specific excited vibrational eigenstate is accomplished. The pulse envelope is constructed such that high intensities are avoided in order to eliminate the process of ionization.

Cycloreversion dynamics of a photochromic molecular switch via one-photon and sequential two-photon excitation

Ultrafast pump-probe (PP) and pump-repump-probe (PReP) measurements examine the ring-opening reaction of a photochromic molecular switch following excitation to the first and higher excited states. Sequential two-photon excitation is a sensitive probe of the excited-state dynamics, because the secondary excitation maps the progress along the S1 reaction coordinate onto the higher excited states of the molecule. In this contribution, secondary excitation at 800 nm accesses more reactive regions of the excited-state potential energy surfaces than are accessible with direct vertical excitation in the visible or UV. The quantum yield for cycloreversion increases by a factor of 3.5 ± 0.9 compared with one-photon excitation when the delay between the 500 nm pump and 800 nm repump laser pulses increases beyond ~100 fs, in contrast with a slower ~3 ps increase that was previously observed for one-color sequential excitation at 500 nm. The evolution of an excited-state absorption band reveals the dynamics of the higher-lying excited state for both one-photon excitation in the UV and sequential two-photon excitation. The spectroscopy and dynamics of the higher-lying excited state are similar for both excitation pathways, including a lifetime of ~100 fs. The complementary PP and PReP measurements provide a detailed picture of the ultrafast excited-state dynamics, including new insight on the role of excited states above S1 in controlling the photochemical cycloreversion reaction.

Mechanisms in environmentally assisted one-photon phase control

The ability of an environment to assist in one-photon phase control relies upon entanglement between the system and bath and on the breaking of the time reversal symmetry. Here, one-photon phase control is examined analytically and numerically in a model system, allowing an analysis of the relative strength of these contributions. Further, the significant role of non-Markovian dynamics and of moderate system-bath coupling in enhancing one-photon phase control is demonstrated, and an explicit role for quantum mechanics is noted in the existence of initial non-zero stationary coherences. Finally, desirable conditions are shown to be required to observe such environmentally assisted control, since the system will naturally equilibrate with its environment at longer times, ultimately resulting in the loss of phase control.

Coherent-control of linear signals: frequency-domain analysis

The dependence of various types of linear signals on the phase profile of broadband optical pulses is examined using fundamental time translation invariance symmetry of multipoint correlation functions. The frequency-domain wave-mixing analysis presented here unifies several arguments made earlier with respect to the conditions whereby coherent control schemes may be used.

Coherent one-photon phase control in closed and open quantum systems: a general master equation approach

The underlying mechanisms for one photon phase control are revealed through a master equation approach. Specifically, two mechanisms are identified, one operating on the laser time scale and the other on the time scale of the system-bath interaction. The effects of the secular and non-secular Markovian approximations are carefully examined.