Coherent Control of Retinal Isomerization in Bacteriorhodopsin

Tracking the conical intersection dynamics for the photoinduced Jahn-Teller switch of a Mn(iii) complex

Octahedral Mn(iii) ions predominantly exhibit an axially elongated Jahn-Teller (JT) distortion, which is responsible for their large uniaxial magnetic anisotropy. As a result, they are often used in the synthesis of single-molecule magnets (SMMs). Modulation of the JT distortion using femtosecond laser pulses could offer a route to controlling the magnetisation direction, and therefore is promising for the development of data storage devices that work on ultrafast timescales. Photoinduced switching of the distortion from an axially elongated to an axially compressed structure has been demonstrated for various Mn(iii) complexes. However, the dynamics around the region of the conical intersection for the photoinduced JT switch remains unclear. Here, ultrafast transient absorption spectra were recorded for solutions of tris(2,2,6,6-tetramethyl-3,5-heptanedionato)manganese(iii) (Mn(dpm)3) in ethanol to further explore the dynamics of the photoinduced JT switch. We observe the generation of a vibrational wavepacket on the excited state surface, which has a frequency of approximately 155 cm-1 and encompasses a JT-active vibrational mode. This coherent motion is maintained after passage through the conical intersection back to the ground state, which launches wavepackets along the ground state potential energy surface (PES) with frequencies of approximately 180 and 110 cm-1 that we assign to the elongated and compressed state, respectively. Inspection of the relative phases of the frequencies reveals phase shifts that are consistent with a one-mode reaction coordinate, and passes through the conical intersection at 1/4 and 3/4 of the excited state vibrational period. Our results provide direct insights into the non-adiabatic dynamics of Mn(iii) complexes, which can be used to guide the synthesis of optically controlled SMMs.

Ultrafast Imaging of Jahn-Teller Distortion and the Correlated Proton Migration in Photoionized Cyclopropane

The Jahn-Teller (JT) distortion is one of the fundamental processes in molecules and condensed phase matters. For photoionized organic molecules with high symmetry, the JT effect leads to geometric instability in certain electron configurations and thus has a significant effect on the subsequent isomerization and proton migration processes. Utilizing the femtosecond pump-probe Coulomb explosion method, we probe the isomerization dynamics process of a monovalent cyclopropane cation (C3H6+) caused by proton migration and reveal the relationship between proton migration and JT distortion. We found that the C3H6+ cation evolves from the D3h symmetric equilateral triangle geometry either to the acute triangle via two elongated C-C bonds (JT1) or to the obtuse triangle via a single elongated C-C bond (JT2). The JT1 pathway does not involve proton migration, while the JT2 pathway drives proton migration and can be mapped into the indirect dissociation channel of Coulomb explosion. The time-resolved experiment indicates that the delay time between those two JT pathways can be as large as ∼600 fs. After the JT distortion, the cyclopropane cation undergoes a subsequent structural evolution, which brings a greater variety of dissociation channels.

Application of density matrix Wigner transforms for ultrafast macromolecular and chemical x-ray crystallography

Time-Resolved Serial Femtosecond Crystallography (TR-SFX) conducted at X-ray Free Electron Lasers (XFELs) has become a powerful tool for capturing macromolecular structural movies of light-initiated processes. As the capabilities of XFELs advance, we anticipate that a new range of coherent control and structural Raman measurements will become achievable. Shorter optical and x-ray pulse durations and increasingly more exotic pulse regimes are becoming available at free electron lasers. Moreover, with high repetition enabled by the superconducting technology of European XFEL (EuXFEL) and Linac Coherent Light Source (LCLS-II) , it will be possible to improve the signal-to-noise ratio of the light-induced differences, allowing for the observation of vibronic motion on the sub-Angstrom level. To predict and assign this coherent motion, which is measurable with a structural technique, new theoretical approaches must be developed. In this paper, we present a theoretical density matrix approach to model the various population and coherent dynamics of a system, which considers molecular system parameters and excitation conditions. We emphasize the use of the Wigner transform of the time-dependent density matrix, which provides a phase space representation that can be directly compared to the experimental positional displacements measured in a TR-SFX experiment. Here, we extend the results from simple models to include more realistic schemes that include large relaxation terms. We explore a variety of pulse schemes using multiple model systems using realistic parameters. An open-source software package is provided to perform the density matrix simulation and Wigner transformations. The open-source software allows us to define any arbitrary level schemes as well as any arbitrary electric field in the interaction Hamiltonian.

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.

Light-Harvesting Efficiency Cannot Depend on Optical Coherence in the Absence of Orientational Order

The coherence of light has been proposed as a quantum-mechanical control for enhancing light-harvesting efficiency. In particular, optical coherence can be manipulated by changing either the polarization state or the spectral phase of the light. Here, we show that, in weak light, light-harvesting efficiency cannot be controlled using any form of optical coherence in molecular light-harvesting systems and, more broadly, those comprising orientationally disordered subunits and operating on longer-than-ultrafast time scales. Under those conditions, optical coherence does not affect the light-harvesting efficiency, meaning that it cannot be used for control. Specifically, polarization-state control is lost in disordered samples or when the molecules reorient on the time scales of light harvesting, and spectral-phase control is lost when the efficiency is time-averaged over a period longer than the optical coherence time. In practice, efficiency is always averaged over long times, meaning that coherent optical control is only possible through polarization and only in systems with orientational order.

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).

Modulated super-Gaussian laser pulse to populate a dark rovibrational state of acetylene

A pulse-shaping technique in the mid-infrared spectral range based on pulses with a super-Gaussian temporal profile is considered for laser control. We show a realistic and efficient path to the population of a dark rovibrational state in acetylene (C2H2). The laser-induced dynamics in C2H2 are simulated using fully experimental structural parameters. Indeed, the rotation-vibration energy structure, including anharmonicities, is defined by the global spectroscopic Hamiltonian for the ground electronic state of C2H2 built from the extensive high-resolution spectroscopy studies on the molecule, transition dipole moments from intensities, and the effects of the (inelastic) collisions that are parameterized from line broadenings using the relaxation matrix [A. Aerts, J. Vander Auwera, and N. Vaeck, J. Chem. Phys. 154, 144308 (2021)]. The approach, based on an effective Hamiltonian, outperforms today's ab initio computations both in terms of accuracy and computational cost for this class of molecules. With such accuracy, the Hamiltonian permits studying the inner mechanism of theoretical pulse shaping [A. Aerts et al., J. Chem. Phys. 156, 084302 (2022)] for laser quantum control. Here, the generated control pulse presents a number of interferences that take advantage of the control mechanism to populate the dark state. An experimental setup is proposed for in-laboratory investigation.

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.

Filming enhanced ionization in an ultrafast triatomic slingshot

Filming atomic motion within molecules is an active pursuit of molecular physics and quantum chemistry. A promising method is laser-induced Coulomb Explosion Imaging (CEI) where a laser pulse rapidly ionizes many electrons from a molecule, causing the remaining ions to undergo Coulomb repulsion. The ion momenta are used to reconstruct the molecular geometry which is tracked over time (i.e., filmed) by ionizing at an adjustable delay with respect to the start of interatomic motion. Results are distorted, however, by ultrafast motion during the ionizing pulse. We studied this effect in water and filmed the rapid "slingshot" motion that enhances ionization and distorts CEI results. Our investigation uncovered both the geometry and mechanism of the enhancement which may inform CEI experiments in many other polyatomic molecules.

From a one-mode to a multi-mode understanding of conical intersection mediated ultrafast organic photochemical reactions

This review discusses how ultrafast organic photochemical reactions are controlled by conical intersections, highlighting that decay to the ground-state at multiple points of the intersection space results in their multi-mode character.

Steady State Photoisomerization Quantum Yield of Model Rhodopsin: Insights from Wavepacket Dynamics?

We simulate the nonequilibrium steady state cis-trans photoisomerization of retinal chromophore in rhodopsin on the basis of a two-state, two-mode model coupled to a thermal environment. By analyzing the systematic trends within an inhomogeneously broadened ensemble of systems, we find that the steady state reaction quantum yield (QY) correlates strongly with the excess energy above the crossing point of the system, in agreement with the prediction of the short-time dynamical wavepacket picture. However, the nontrivial dependence of the QY on the system-environment interaction indicates that a pure dynamical picture is insufficient and that environment-induced partial internal energy redistribution takes place before the reaction concludes. These results imply that a proper treatment of the photoisomerization reaction, particularly its high QY, must account for the redistribution and dissipation of energy beyond the dynamical wavepacket motion that is typically employed in the literature and that is appropriate only in the transient regime.

Single molecule kinetics of bacteriorhodopsin by HS-AFM

Bacteriorhodopsin is a seven-helix light-driven proton-pump that was structurally and functionally extensively studied. Despite a wealth of data, the single molecule kinetics of the reaction cycle remain unknown. Here, we use high-speed atomic force microscopy methods to characterize the single molecule kinetics of wild-type bR exposed to continuous light and short pulses. Monitoring bR conformational changes with millisecond temporal resolution, we determine that the cytoplasmic gate opens 2.9 ms after photon absorption, and stays open for proton capture for 13.2 ms. Surprisingly, a previously active protomer cannot be reactivated for another 37.6 ms, even under excess continuous light, giving a single molecule reaction cycle of ~20 s⁻¹. The reaction cycle slows at low light where the closed state is prolonged, and at basic or acidic pH where the open state is extended.

Here, the authors use high-speed atomic force microscopy (HS-AFM) methods to characterize the single molecule kinetics of wild-type bacteriorhodopsin (bR) with millisecond temporal resolution, providing new insights into the bR conformational cycle.

Untargeted effects in organic exciton-polariton transient spectroscopy: A cautionary tale

Strong light-matter coupling to form exciton- and vibropolaritons is increasingly touted as a powerful tool to alter the fundamental properties of organic materials. It is proposed that these states and their facile tunability can be used to rewrite molecular potential energy landscapes and redirect photophysical pathways, with applications from catalysis to electronic devices. Crucial to their photophysical properties is the exchange of energy between coherent, bright polaritons and incoherent dark states. One of the most potent tools to explore this interplay is transient absorption/reflectance spectroscopy. Previous studies have revealed unexpectedly long lifetimes of the coherent polariton states, for which there is no theoretical explanation. Applying these transient methods to a series of strong-coupled organic microcavities, we recover similar long-lived spectral effects. Based on transfer-matrix modeling of the transient experiment, we find that virtually the entire photoresponse results from photoexcitation effects other than the generation of polariton states. Our results suggest that the complex optical properties of polaritonic systems make them especially prone to misleading optical signatures and that more challenging high-time-resolution measurements on high-quality microcavities are necessary to uniquely distinguish the coherent polariton dynamics.

Attochemistry: Is Controlling Electrons the Future of Photochemistry?

Controlling matter with light has always been a great challenge, leading to the ever-expanding field of photochemistry. In addition, since the first generation of light pulses of attosecond (1 as = 10^-18 s) duration, a great deal of effort has been devoted to observing and controlling electrons on their intrinsic time scale. Because of their short duration, attosecond pulses have a large spectral bandwidth populating several electronically excited states in a coherent manner, i.e., an electronic wavepacket. Because of interference, such a wavepacket has a new electronic distribution implying a potentially different and totally new reactivity as compared to traditional photochemistry, leading to the novel concept of "attochemistry". This nascent field requires the support of theory right from the start. In this Perspective, we discuss the opportunities offered by attochemistry, the related challenges, and the current and future state-of-the-art developments in theoretical chemistry needed to model it accurately.

Diffractive Imaging of Conical Intersections Amplified by Resonant Infrared Fields

The fate of virtually all photochemical reactions is determined by conical intersections. These are energetically degenerate regions of molecular potential energy surfaces that strongly couple electronic states, thereby enabling fast relaxation channels. Their direct spectroscopic detection relies on weak features that are often buried beneath stronger, less interesting contributions. For azobenzene photoisomerization, a textbook photochemical reaction, we demonstrate how a resonant infrared field can be employed during the conical intersection passage to significantly enhance its coherence signatures in time-resolved X-ray diffraction while leaving the product yield intact. This transition-state amplification holds promise to bring signals of conical intersections above the detection threshold.

Selective Enhancement of Spectroscopic Features by Quantum Optimal Control

Tailored light can be used to steer atomic motions into selected quantum pathways. In optimal control theory (OCT), the target is usually expressed in terms of the molecular wave function, a quantity that is not directly observable in experiment. We present simulations using OCT that optimize the spectroscopic signal itself. By shaping the optical pump, the x-ray stimulated Raman signal, which occurs solely during the passage through conical intersections, is temporally controlled and amplified by up to 2 orders of magnitude. This enhancement can be crucial in order to bring small coherence-based signatures above the detectable threshold. Our approach is applicable to any signal that depends on the expectation value of a positive definite operator.

Extreme Parametric Sensitivity in the Steady-State Photoisomerization of Two-Dimensional Model Rhodopsin

We computationally studied the photoisomerization reaction of the retinal chromophore in rhodopsin using a two-state two-mode model coupled to thermal baths. Reaction quantum yields at the steady state (10 ps and beyond) were found to be considerably different than their transient values, suggesting a weak correlation between transient and steady-state dynamics in these systems. Significantly, the steady-state quantum yield was highly sensitive to minute changes in system parameters, while transient dynamics was nearly unaffected. Correlation of such sensitivity with standard level spacing statistics of the nonadiabatic vibronic system suggests a possible origin in quantum chaos. The significance of this observation of quantum yield parametric sensitivity in biological models of vision has profound conceptual and fundamental implications.

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.

On Weak-Field (One-Photon) Coherent Control of Photoisomerization

Photochemistry induced by phase-coherent laser light is an intriguing topic. The possibility of weak-field (one-photon) phase-only control of photoisomerization is controversial. Experimental studies on the weak-field coherent control of cis-trans isomerization have led to conflicting results. Here we address this issue by quantum dynamical calculations, focusing on a mechanism where different "phase-shaped" wave packets are quickly stabilized ("dumped") in the trans configuration because of prompt energy dissipation. We systematically investigate different relaxation rates with the system-bath dynamics described within the time-dependent Hartree approximation leading to a friction-type force. We find evidence for phase control of trans-isomer yields (about 5%) in this model with pure energy dissipation given sufficiently strong dampening.

Uncovering the Functional Role of Coherent Phonons during the Photoinduced Phase Transition in a Molecular Crystal

The atomic motions that make up phonons and molecular vibrations in molecular crystals influence their photophysical and electronic properties, including polaron formation, carrier mobility, and phase transitions. Discriminating between spectator and driving motions is a significant challenge hindering optimization. Unlocking this information and developing fine-tuned controls over actively participating phonon modes would not only lead to a stronger understanding of photochemistry but also provide a significant new tool in controlling solid state chemistry. We present a strategy using rationally designed double pulses to unveil the unique function of specific excited state phonon modes. Using ultrafast spectroscopy, we identified 50 and 90 cm^-1 phonons involved in modulating the photoinduced spin-Peierls melting of potassium tetracyanoquinodimethane crystals. We show that the 50 cm^-1 phonon specifically corresponds to the coherent nuclear wavepacket involved in the charge transfer component of the overall spin-Peierls phase melting process, while the 90 cm^-1 phonon facilitates the phase transition component.

Sub-cycle atomic-scale forces coherently control a single-molecule switch

Scanning probe techniques can leverage atomically precise forces to sculpt matter at surfaces, atom by atom. These forces have been applied quasi-statically to create surface structures^1-7 and influence chemical processes^8,9, but exploiting local dynamics^10-14 to realize coherent control on the atomic scale remains an intriguing prospect. Chemical reactions^15-17, conformational changes^18,19 and desorption²⁰ have been followed on ultrafast timescales, but directly exerting femtosecond forces on individual atoms to selectively induce molecular motion has yet to be realized. Here we show that the near field of a terahertz wave confined to an atomically sharp tip provides femtosecond atomic-scale forces that selectively induce coherent hindered rotation in the molecular frame of a bistable magnesium phthalocyanine molecule. Combining lightwave-driven scanning tunnelling microscopy^21-24 with ultrafast action spectroscopy^10,13, we find that the induced rotation modulates the probability of the molecule switching between its two stable adsorption geometries by up to 39 per cent. Mapping the response of the molecule in space and time confirms that the force acts on the atomic scale and within less than an optical cycle (that is, faster than an oscillation period of the carrier wave of light). We anticipate that our strategy might ultimately enable the coherent manipulation of individual atoms within single molecules or solids so that chemical reactions and ultrafast phase transitions can be manipulated on their intrinsic spatio-temporal scales.

Effects of high pulse intensity and chirp in two-dimensional electronic spectroscopy of an atomic vapor

The effects of high pulse intensity and chirp on two-dimensional electronic spectroscopy signals are experimentally investigated in the highly non-perturbative regime using atomic rubidium vapor as clean model system. Data analysis is performed based on higher-order Feynman diagrams and non-perturbative numerical simulations of the system response. It is shown that higher-order contributions may lead to a fundamental change of the static appearance and beating-maps of the 2D spectra and that chirped pulses enhance or suppress distinct higher-order pathways. We further give an estimate of the threshold intensity beyond which the high-intensity effects become visible for the system under consideration.

Efficient Conversion of Light to Chemical Energy: Directional, Chiral Photoswitches with Very High Quantum Yields

Photochromic systems have been used to achieve a number of engineering functions such as light energy conversion, molecular motors, pumps, actuators, and sensors. Key to practical applications is a high efficiency in the conversion of light to chemical energy, a rigid structure for the transmission of force to the environment, and directed motion during isomerization. We present a novel type of photochromic system (diindane diazocines) that converts visible light with an efficiency of 18 % to chemical energy. Quantum yields are exceptionally high with >70 % for the cis-trans isomerization and 90 % for the back-reaction and thus higher than the biochemical system rhodopsin (64 %). Two diastereomers (meso and racemate) were obtained in only two steps in high yields. Both isomers are directional switches with high conversion rates (76-99 %). No fatigue was observed after several thousands of switching cycles in both systems.

Pulsed two-photon coherent control of channelrhodopsin-2 photocurrent in live brain cells

Channelrhodopsin-2 (ChR2) is an ion channel activated by the absorption of light. A recent experiment demonstrated that the current emanating from neurons in live brain cells expressing ChR2 can be controlled using two-photon phase control. Here, we propose an experimentally testable coherent control mechanism for this phenomenon. Significantly, we describe how femtosecond, quantum coherent processes arising from weak-field ultrafast excitation are responsible for the reported control of the millisecond classical dynamics of the neuronal current.

Photoinduced Forward and Backward Pedalo-Type Motion of a Molecular Switch

Photoresponsive molecular switches enable spatial and temporal control of molecular processes and are therefore crucial for the development of smart functional materials. Because the light-induced dynamics of these switching units are at the core of the resulting functionality, a detailed insight into their structural time evolution is fundamental for molecular embedding. Here, we performed a hybrid quantum mechanics (CASPT2 and TDDFT)/molecular mechanics (QM/MM) study to elucidate the photodynamics of an azodicarboxamide-based molecular switch, which is a promising candidate for implementation in highly dense environments such as polymers. In particular, we report a detailed picture of the molecular motion at the atomic level based on a relevant number of excited-state trajectories. We show that the azodicarboxamide-based molecular switch undergoes both a forward and backward pedalo-type motion upon excitation. Trans-cis photoisomerization on the other hand, which is well-known to occur for other azo-based chromophores, is shown to be a negligible pathway. By validating the volume-conserving pedalo-type motion, we provide a rational basis for the design of novel types of photoresponsive functional materials in which the active component must operate in a confined space.

Super-resolution nanoscopy by coherent control on nanoparticle emission

Super-resolution nanoscopy based on wide-field microscopic imaging provided high efficiency but limited resolution. Here, we demonstrate a general strategy to push its resolution down to ~50 nm, which is close to the range of single molecular localization microscopy, without sacrificing the wide-field imaging advantage. It is done by actively and simultaneously modulating the characteristic emission of each individual emitter at high density. This method is based on the principle of excited state coherent control on single-particle two-photon fluorescence. In addition, the modulation efficiently suppresses the noise for imaging. The capability of the method is verified both in simulation and in experiments on ZnCdS quantum dot-labeled films and COS7 cells. The principle of coherent control is generally applicable to single-multiphoton imaging and various probes.

Observation of an isomerizing double-well quantum system in the condensed phase

Molecular isomerization fundamentally involves quantum states bound within a potential energy function with multiple minima. For isolated gas-phase molecules, eigenstates well above the isomerization saddle points have been characterized. However, to observe the quantum nature of isomerization, systems in which transitions between the eigenstates occur-such as condensed-phase systems-must be studied. Efforts to resolve quantum states with spectroscopic tools are typically unsuccessful for such systems. An exception is CO adsorbed on NaCl(100), which is bound with the well-known OC-Na⁺ structure. We observe an unexpected upside-down isomer (CO-Na⁺) produced by infrared laser excitation and obtain well-resolved infrared fluorescence spectra from highly energetic vibrational states of both orientational isomers. This distinctive condensed-phase system is ideally suited to spectroscopic investigations of the quantum nature of isomerization.

Time-resolved serial femtosecond crystallography at the European XFEL

The European XFEL (EuXFEL) is a 3.4 km long X-ray source, which produces femtosecond, ultra-brilliant and spatially coherent X-ray pulses at megahertz repetition rates. This X-ray source has been designed to enable the observation of ultrafast processes with near-atomic spatial resolution. Time-resolved crystallographic investigations on biological reactions constitute a particularly important class of experiments with biomedical and health related implications. Due to the unusual X-ray pulse structure, such an experiment is challenging. Here we demonstrate how a biological reaction can be followed on ultrafast time scales at the EuXFEL. We investigate the picosecond time range in the photocycle of photoactive yellow protein (PYP) with MHz X-ray pulse rates. We show that difference electron density maps of excellent quality can be obtained. Results connect the previously explored femtosecond PYP dynamics to time scales accessible at synchrotrons. This opens the door to a wide range of time resolved studies at the EuXFEL.

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.

Effect of point mutations on the ultrafast photo-isomerization of Anabaena sensory rhodopsin

Anabaena sensory rhodopsin (ASR) is a particular microbial retinal protein for which light-adaptation leads to the ability to bind both the all-trans, 15-anti (AT) and the 13-cis, 15-syn (13C) isomers of the protonated Schiff base of retinal (PSBR). In the context of obtaining insight into the mechanisms by which retinal proteins catalyse the PSBR photo-isomerization reaction, ASR is a model system allowing to study, within the same protein, the protein-PSBR interactions for two different PSBR conformers at the same time. A detailed analysis of the vibrational spectra of AT and 13C, and their photo-products in wild-type ASR obtained through femtosecond (pump-) four-wave-mixing is reported for the first time, and compared to bacterio- and channelrhodopsin. As part of an extensive study of ASR mutants with blue-shifted absorption spectra, we present here a detailed computational analysis of the origin of the mutation-induced blue-shift of the absorption spectra, and identify electrostatic interactions as dominating steric effects that would entail a red-shift. The excited state lifetimes and isomerization reaction times (IRT) for the three mutants V112N, W76F, and L83Q are studied experimentally by femtosecond broadband transient absorption spectroscopy. Interestingly, in all three mutants, isomerization is accelerated for AT with respect to wild-type ASR, and this the more, the shorter the wavelength of maximum absorption. On the contrary, the 13C photo-reaction is slightly slowed down, leading to an inversion of the ESLs of AT and 13C, with respect to wt-ASR, in the blue-most absorbing mutant L83Q. Possible mechanisms for these mutation effects, and their steric and electrostatic origins are discussed.

Spatiotemporal observations of light propagation in multiple polarization states

Real-time imaging techniques involving light propagation are commonly applied in the fields of physics, chemistry, and biomedicine. However, conventional techniques provide only the intensity change associated with light propagation. Here, we propose an imaging technique to visualize the ultrafast behavior of the polarization state of a propagating light pulse with four different linear polarization components. This approach provides ultrahigh temporal resolution to observe the light in motion. We recorded a motion picture of a three-dimensional image of a light pulse propagating through a diffuser and a calcite crystal at 56.8 and 75.4 ps, respectively. This technique can contribute to revealing the polarization state of propagating light pulses in a medium and ultrafast phenomenon.

Time-Resolved Macromolecular Crystallography at Pulsed X-ray Sources

The focus of structural biology is shifting from the determination of static structures to the investigation of dynamical aspects of macromolecular function. With time-resolved macromolecular crystallography (TRX), intermediates that form and decay during the macromolecular reaction can be investigated, as well as their reaction dynamics. Time-resolved crystallographic methods were initially developed at synchrotrons. However, about a decade ago, extremely brilliant, femtosecond-pulsed X-ray sources, the free electron lasers for hard X-rays, became available to a wider community. TRX is now possible with femtosecond temporal resolution. This review provides an overview of methodological aspects of TRX, and at the same time, aims to outline the frontiers of this method at modern pulsed X-ray sources.

Two-dimensional electronic-vibrational spectroscopic study of conical intersection dynamics: an experimental and electronic structure study

The relaxation from the lowest singlet excited state of the triphenylmethane dyes, crystal violet and malachite green, is studied via two-dimensional electronic-vibrational (2DEV) spectroscopy.

Excited State Vibrational Spectra of All- trans Retinal Derivatives in Solution Revealed By Pump-DFWM Experiments

The ultrafast structural changes during the photoinduced isomerization of the retinal-protonated Schiff base (RPSB) is still a poorly understood aspect in the retinal's photochemistry. In this work, we apply pump-degenerate four-wave mixing (pump-DFWM) to all- trans retinal (ATR) and retinal Schiff bases (RSB) to resolve coherent high- and low-frequency vibrational signatures from excited electronic states. We show that the vibrational spectra of excited singlet states in these samples exhibit pronounced differences compared to the relaxed ground state. Pump-DFWM results indicate three major features for ATR and RSB. (i) Excited state vibrational spectra of ATR and RSB consist predominately of low-frequency modes in the energetic range 100-500 cm^-1. (ii) Excited state vibrational spectra show distinct differences for excitation in specific regions of electronic transitions of excited state absorption and emission. (iii) Low-frequency modes in ATR and RSB are inducible during the entire lifetime of the excited electronic states. This latter effect points to a transient molecular structure that, following initial relaxation between different excited electronic states, does not change anymore over the lifetime of the finally populated excited electronic state.

Coherent phenomena in photosynthetic light harvesting: part two-observations in biological systems

Considerable debate surrounds the question of whether or not quantum mechanics plays a significant, non-trivial role in photosynthetic light harvesting. Many have proposed that quantum superpositions and/or quantum transport phenomena may be responsible for the efficiency and robustness of energy transport present in biological systems. The critical experimental observations comprise the observation of coherent oscillations or "quantum beats" via femtosecond laser spectroscopy, which have been observed in many different light harvesting systems. Part Two of this review aims to provide an overview of experimental observations of energy transfer in the most studied light harvesting systems. Length scales, derived from crystallographic studies, are combined with energy and time scales of the beats observed via spectroscopy. A consensus is emerging that most long-lived (hundreds of femtoseconds) coherent phenomena are of vibrational or vibronic origin, where the latter may result in coherent excitation transport within a protein complex. In contrast, energy transport between proteins is likely to be incoherent in nature. The question of whether evolution has selected for these non-trivial quantum phenomena may be an unanswerable question, as dense packings of chromophores will lead to strong coupling and hence non-trivial quantum phenomena. As such, one cannot discern whether evolution has optimised light harvesting systems for high chromophore density or for the ensuing quantum effects as these are inextricably linked and cannot be switched off.

Pathways to New Applications for Quantum Control

In 1998, the first successful quantum control experiment with application to a molecular framework was conducted with a shaped laser pulse, optimizing the branching ratio between different organometallic reaction channels. This work induced a vast activity in quantum control during the next 10 years, and different optimization aims were achieved in the gas phase, liquid phase, and even in biologically relevant molecules like light-harvesting complexes. Accompanying and preceding this development were important advances in theoretical quantum control simulations. They predicted several control scenarios and explained how and why quantum control experiments work. After many successful proofs of concept in molecular science, the big challenge is to expand its huge conceptual potential of directly being able to steer nuclear and/or electronic motion to more applied implementations. In this Account, based on several recent advances, we give a personal evaluation of where the field of molecular quantum control is at the moment and especially where we think promising applications can be in the near future. One of these paths leads to synthetic chemistry. The synthesis of novel pharmaceutical compounds or natural products often involves many synthetic steps, each one devouring resources and lowering the product yield. Shaped laser pulses can possibly act as photonic reagents and shorten the synthetic route toward the desired product. Chemical synthesis usually takes place in solution, and by including explicit solvent molecules in our quantum control simulations, we were able to identify their highly inhomogeneous influence on chemical reactions and how this affects potential quantum control. More important, we demonstrated for a synthetically relevant example that these complications can be overcome in theory, and laser pulses can be optimized to initiate the desired carbon-carbon bond formation. Putting this into context with the recently emerging concept of flow chemistry, which brings several practical advantages to the application of laser pulses, we want to encourage experimental groups to exploit this concept. Another path was opened by several additions to the commonly used laser pulse optimization algorithm (optimal control theory, OCT), several of which were developed in our group. The OCT algorithm as such is a purely mathematical optimization procedure, with no direct relation to experimental requirements. This means that usually the electric fields obtained out of OCT optimizations do not resemble laser pulses that can be achieved experimentally. However, the previously mentioned additions are aimed at closing the gap toward the experiment. In a recent quantum control study of our group, these algorithmic developments came to fruition. We were able to suggest a shaped laser pulse which can induce a long-living wave packet in the excited state of uracil. This might pave the way for novel experiments dedicated to investigating the formation of biological photodamage in DNA and RNA. The pulse we suggest is surprisingly simple because of the extended OCT algorithm and fulfills all criteria to be experimentally accessible.

Observation of Quantum Interference and Coherent Control in a Photochemical Reaction

Coherent control of reactants remains a long-standing challenge in quantum chemistry. In particular, we have studied laser-induced molecular formation (photoassociation) in a Raman-dressed spin-orbit-coupled ^{87}Rb Bose-Einstein condensate, whose spin quantum state is a superposition of multiple bare spin components. In contrast to the notably different photoassociation-induced fractional atom losses observed for the bare spin components of a statistical mixture, a superposition state with a comparable spin composition displays the same fractional loss on every spin component. We interpret this as the superposition state itself undergoing photoassociation. For superposition states induced by a large Raman coupling and zero Raman detuning, we observe a nearly complete suppression of the photoassociation rate. This suppression is consistent with a model based upon quantum destructive interference between two photoassociation pathways for colliding atoms with different spin combinations. This model also explains the measured dependence of the photoassociation rate on the Raman detuning at a moderate Raman coupling. Our work thus suggests that preparing atoms in quantum superpositions may represent a powerful new technique to coherently control photochemical reactions.

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.

Spiers Memorial Lecture. Introductory lecture: the impact of structure on photoinduced processes in nucleic acids and proteins

Light is an important environmental variable and most organisms have evolved means to sense, exploit or avoid it and to repair detrimental effects on their genome. In general, light absorption is the task of specific chromophores, however other biomolecules such as oligonucleotides also do so which can result in undesired outcomes such as mutations and cancer. Given the biological importance of light-induced processes and applications for imaging, optogenetics, photodynamic therapy or photovoltaics, there is a great interest in understanding the detailed molecular mechanisms of photoinduced processes in proteins and nucleic acids. The processes are typically characterized by time-resolved spectroscopic approaches or computation, inferring structural information on transient species from stable ground state structures. Recently, however, structure determination of excited states or other short-lived species has become possible with the advent of X-ray free-electron lasers. This review gives an overview of the impact of structure on the understanding of photoinduced processes in macromolecules, focusing on systems presented at this Faraday Discussion meeting.