The Ultrafast Photoisomerizations of Rhodopsin and Bathorhodopsin Are Modulated by Bond Length Alternation and HOOP Driven Electronic Effects

Comparative quantum-classical dynamics of natural and synthetic molecular rotors show how vibrational synchronization modulates the photoisomerization quantum efficiency

We use quantum-classical trajectories to investigate the origin of the different photoisomerization quantum efficiency observed in the dim-light visual pigment Rhodopsin and in the light-driven biomimetic molecular rotor para-methoxy N-methyl indanylidene-pyrrolinium (MeO-NAIP) in methanol. Our results reveal that effective light-energy conversion requires, in general, an auxiliary molecular vibration (called promoter) that does not correspond to the rotary motion but synchronizes with it at specific times. They also reveal that Nature has designed Rhodopsin to exploit two mechanisms working in a vibrationally coherent regime. The first uses a wag promoter to ensure that ca. 75% of the absorbed photons lead to unidirectional rotations. The second mechanism ensures that the same process is fast enough to avoid directional randomization. It is found that MeO-NAIP in methanol is incapable of exploiting the above mechanisms resulting into a 50% quantum efficiency loss. However, when the solvent is removed, MeO-NAIP rotation is predicted to synchronize with a ring-inversion promoter leading to a 30% increase in quantum efficiency and, therefore, biomimetic behavior.

Color Tuning in Bovine Rhodopsin through Polarizable Embedding

Bovine rhodopsin is among the most studied proteins in the rhodopsin family. Its primary activation mechanism is the photoisomerization of 11-cis retinal, triggered by the absorption of a UV-visible photon. Different mutants of the same rhodopsin show different absorption wavelengths due to the influence of the specific amino acid residues forming the cavity in which the retinal chromophore is embedded, and rhodopsins activated at different wavelengths are, for example, exploited in the field of optogenetics. In this letter, we present a procedure for systematically investigating color tuning in models of bovine rhodopsin and a set of its mutants embedded in a membrane bilayer. Vertical excitation energy calculations were carried out with the polarizable embedding potential for describing the environment surrounding the chromophore. We show that polarizable embedding outperformed regular electrostatic embedding in determining both the vertical excitation energies and associated oscillator strengths of the systems studied.

Potential energy interpolation with target-customized weighting coordinates: application to excited-state dynamics of photoactive yellow protein chromophore in water

Interpolation of potential energy surfaces (PESs) can provide a practical route to performing molecular dynamics simulations with a reliability matching a high-level quantum chemical calculation. An obstacle to its widespread use is perhaps the lack of general and optimal interpolation settings that can be applied in a black-box manner for any given molecular system. How to set up the weights for interpolation is one such task, and we still need to diversify the approaches in order to treat various systems. Here, we develop a new interpolation weighting scheme, which allows us to choose the weighting coordinates in a system-specific manner, by amplifying the contribution from specific internal coordinates. The new weighting scheme with an appropriate selection of coordinates is proved to be effective in reducing the interpolation error along the reaction pathway. As a demonstration, we consider the photoactive yellow protein chromophore system, as it constitutes itself as an interesting target that bears long-standing questions related to excited-state dynamics inside protein environments. We build its two-state diabatic interpolated PES with the new weighting scheme. We indeed see the utility of our scheme by conducting nonadiabatic molecular dynamics simulations with the required semi-global PES based on a limited number of data points.

Deciphering Photoreceptors Through Atomistic Modeling from Light Absorption to Conformational Response

In this review, we discuss the successes and challenges of the atomistic modeling of photoreceptors. Throughout our presentation, we integrate explanations of the primary methodological approaches, ranging from quantum mechanical descriptions to classical enhanced sampling methods, all while providing illustrative examples of their practical application to specific systems. To enhance the effectiveness of our analysis, our primary focus has been directed towards the examination of applications across three distinct photoreceptors. These include an example of Blue Light-Using Flavin (BLUF) domains, a bacteriophytochrome, and the orange carotenoid protein (OCP) employed by cyanobacteria for photoprotection. Particular emphasis will be placed on the pivotal role played by the protein matrix in fine-tuning the initial photochemical event within the embedded chromophore. Furthermore, we will investigate how this localized perturbation initiates a cascade of events propagating from the binding pocket throughout the entire protein structure, thanks to the intricate network of interactions between the chromophore and the protein.

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

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

A Nitrogen Out-of-Plane (NOOP) Mechanism for Imine-Based Light-Driven Molecular Motors

Light-driven molecular motors have generated considerable interest due to their potential applications in material and biological systems. Recently, Greb and Lehn reported a new class of molecular motors, chiral N-alkyl imines, which undergo unidirectional rotation induced by light and heat. The mechanism of unidirectional motion in molecular motors containing a C═N group has been assumed to consist of photoinduced torsion about the double bond. In this work, we present a computational study of the photoisomerization dynamics of a chiral N-alkyl imine motor. We find that the location and energetics of minimal energy conical intersections (MECIs) alone are insufficient to understand the mechanism of the motor. Furthermore, a key part of the mechanism consists of out-of-plane distortions of the N atom (followed by isomerization about the double bond). Dynamic effects and out-of-plane distortions are critical to understand the observed (rather low) quantum yield for photoisomerization. Our results provide hints as to how the photoisomerization quantum yield might be increased, improving the efficiency of this class of molecular motors.

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.

The involvement of triplet states in the isomerization of retinaloids

Rhodopsins form a family of photoreceptor proteins which utilize the retinal chromophore for light energy conversion. Upon light absorption the retinal chromophore undergoes a photoisomerization. This reaction involves a non-radiative relaxation through a conical intersection between the singlet excited state and the ground state. In this work we studied the possible involvement of triplet states in the photoisomerization of retinaloids using the extended multistate (XMS) version of CASPT2. To this end, truncated models of three retinaloids were considered: protonated Schiff base, deprotonated Schiff base and the aldehyde form. The optimized geometries of the reactant, the product and the conical intersection were connected by a linear interpolation of internal coordinates to describe the isomerization. The energetic position of the low-lying singlet and triplet states as well as their spin-orbit coupling matrix elements (SOCME) were calculated along the isomerization profile. The SOCME values peaked in vicinity of the conical intersection for all the retinaloids. Furthermore, the magnitude of SOCME is invariant to the number of double bonds in the model. The SOCME for the protonated Schiff base is negligible (1.5 cm^-1) which renders the involvement of the triplet state as improbable. However, the largest SOCME value of 30 cm^-1 was found for the aldehyde form, followed by 15 cm^-1 for the deprotonated Schiff base.

On the fluorescence enhancement of arch neuronal optogenetic reporters

The lack of a theory capable of connecting the amino acid sequence of a light-absorbing protein with its fluorescence brightness is hampering the development of tools for understanding neuronal communications. Here we demonstrate that a theory can be established by constructing quantum chemical models of a set of Archaerhodopsin reporters in their electronically excited state. We found that the experimentally observed increase in fluorescence quantum yield is proportional to the computed decrease in energy difference between the fluorescent state and a nearby photoisomerization channel leading to an exotic diradical of the protein chromophore. This finding will ultimately support the development of technologies for searching novel fluorescent rhodopsin variants and unveil electrostatic changes that make light emission brighter and brighter.

Different timescales during ultrafast stilbene isomerization in the gas and liquid phases revealed using time-resolved photoelectron spectroscopy

Directly contrasting ultrafast excited-state dynamics in the gas and liquid phases is crucial to understanding the influence of complex environments. Previous studies have often relied on different spectroscopic observables, rendering direct comparisons challenging. Here, we apply extreme-ultraviolet time-resolved photoelectron spectroscopy to both gaseous and liquid cis-stilbene, revealing the coupled electronic and nuclear dynamics that underlie its isomerization. Our measurements track the excited-state wave packets from excitation along the complete reaction path to the final products. We observe coherent excited-state vibrational dynamics in both phases of matter that persist to the final products, enabling the characterization of the branching space of the S₁-S₀ conical intersection. We observe a systematic lengthening of the relaxation timescales in the liquid phase and a red shift of the measured excited-state frequencies that is most pronounced for the complex reaction coordinate. These results characterize in detail the influence of the liquid environment on both electronic and structural dynamics during a complete photochemical transformation.

Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering

The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.

Charge-Transfer Excitations within Density Functional Theory: How Accurate Are the Most Recommended Approaches?

The performance of the most recent density functionals is assessed for charge-transfer (CT) excitations using comprehensive intra- and intermolecular CT benchmark sets with high-quality reference values. For this comparison, the state-of-the-art range-separated (RS) and long-range-corrected (LC) double hybrid (DH) approaches are selected, and global DH and LC hybrid functionals are also inspected. The correct long-range behavior of the exchange-correlation (XC) energy is extensively studied, and various CT descriptors are compared as well. Our results show that the most robust performance is attained by RS-PBE-P86/SOS-ADC(2), as it is suitable to describe both types of CT excitations with outstanding accuracy. Furthermore, concerning the intramolecular transitions, unexpectedly excellent results are obtained for most of the global DHs, but their limitations are also demonstrated for bimolecular complexes. Despite the outstanding performance of the LC-DH methods for common intramolecular excitations, serious deficiencies are pointed out for intermolecular CT transitions, and the wrong long-range behavior of the XC energy is revealed. The application of LC hybrids to such transitions is not recommended in any respect.

Quantum-classical simulations of rhodopsin reveal excited-state population splitting and its effects on quantum efficiency

The activation of rhodopsin, the light-sensitive G-protein coupled receptor responsible for dim-light vision in vertebrates, is driven by an ultrafast excited-state double-bond isomerization with a quantum efficiency of almost 70%. The origin of such light sensitivity is not understood and a key question is whether in-phase nuclear motion controls the quantum efficiency value. Here, we use hundreds of quantum-classical trajectories to show that, 15 femtoseconds after light absorption, a degeneracy between the reactive excited state and a neighboring state causes the splitting of the rhodopsin population into subpopulations. These subpopulations propagate with different velocities and lead to distinct contributions to the quantum efficiency. We also show that such splitting is modulated by protein electrostatics, thus linking amino-acid sequence variations to quantum efficiency modulation. Finally, we discuss how such a linkage that in principle could be exploited to achieve higher quantum efficiencies, would simultaneously increase the receptor thermal noise leading to a trade-off that may have played a role in rhodopsin evolution.

Internal conversion of the anionic GFP chromophore: in and out of the I-twisted S1/S0 conical intersection seam

The functional diversity of the green fluorescent protein (GFP) family is intimately connected to the interplay between competing photo-induced transformations of the chromophore motif, anionic p-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI^-). Its ability to undergo Z/E-isomerization is of particular importance for super-resolution microscopy and emerging opportunities in optogenetics. Yet, key dynamical features of the underlying internal conversion process in the native HBDI^- chromophore remain largely elusive. We investigate the intrinsic excited-state behavior of isolated HBDI^- to resolve competing decay pathways and map out the factors governing efficiency and the stereochemical outcome of photoisomerization. Based on non-adiabatic dynamics simulations, we demonstrate that non-selective progress along the two bridge-torsional (i.e., phenolate, P, or imidazolinone, I) pathways accounts for the three decay constants reported experimentally, leading to competing ultrafast relaxation primarily along the I-twisted pathway and S₁ trapping along the P-torsion. The majority of the population (∼70%) is transferred to S₀ in the vicinity of two approximately enantiomeric minima on the I-twisted intersection seam (MECI-Is). Despite their sloped, reactant-biased topographies (suggesting low photoproduct yields), we find that decay through these intersections leads to products with a surprisingly high quantum yield of ∼30%. This demonstrates that E-isomer generation results at least in part from direct isomerization on the excited state. A photoisomerization committor analysis reveals a difference in intrinsic photoreactivity of the two MECI-Is and that the observed photoisomerization is the combined result of two effects: early, non-statistical dynamics around the less reactive intersection followed by later, near-statistical behavior around the more reactive MECI-I. Our work offers new insight into internal conversion of HBDI^- that both establishes the intrinsic properties of the chromophore and enlightens principles for the design of chromophore derivatives and protein variants with improved photoswitching properties.

A study of the photochemical behaviour and relaxation mechanisms of anti–syn isomerisation around quinazolinone –N–N bonds

High-resolution NMR experiments revealed that differently substituted quinazolinone-based Schiff bases undergo anti to syn isomerisation on exposure to ultraviolet light in DMSO solution.

Control of Protonated Schiff Base Excited State Decay within Visual Protein Mimics: A Unified Model for Retinal Chromophores

Artificial biomimetic chromophore-protein complexes inspired by natural visual pigments can feature color tunability across the full visible spectrum. However, control of excited state dynamics of the retinal chromophore, which is of paramount importance for technological applications, is lacking due to its complex and subtle photophysics/photochemistry. Here, ultrafast transient absorption spectroscopy and quantum mechanics/molecular mechanics simulations are combined for the study of highly tunable rhodopsin mimics, as compared to retinal chromophores in solution. Conical intersections and transient fluorescent intermediates are identified with atomistic resolution, providing unambiguous assignment of their ultrafast excited state absorption features. The results point out that the electrostatic environment of the chromophore, modified by protein point mutations, affects its excited state properties allowing control of its photophysics with same power of chemical modifications of the chromophore. The complex nature of such fine control is a fundamental knowledge for the design of bio-mimetic opto-electronic and photonic devices.

Effect of charge-transfer enhancement on the efficiency and rotary mechanism of an oxindole-based molecular motor

Harvesting energy and converting it into mechanical motion forms the basis for both natural and artificial molecular motors. Overcrowded alkene-based light-driven rotary motors are powered through sequential photochemical and thermal steps. The thermal helix inversion steps are well characterised and can be manipulated through adjustment of the chemical structure, however, the insights into the photochemical isomerisation steps still remain elusive. Here we report a novel oxindole-based molecular motor featuring pronounced electronic push-pull character and a four-fold increase of the photoisomerization quantum yield in comparison to previous motors of its class. A multidisciplinary approach including synthesis, steady-state and transient absorption spectroscopies, and electronic structure modelling was implemented to elucidate the excited state dynamics and rotary mechanism. We conclude that the charge-transfer character of the excited state diminishes the degree of pyramidalisation at the alkene bond during isomerisation, such that the rotational properties of this oxindole-based motor stand in between the precessional motion of fluorene-based molecular motors and the axial motion of biomimetic photoswitches.

Electrostatic Control of Photoisomerization in Channelrhodopsin 2

Channelrhodopsin 2 (ChR2) is the most commonly used tool in optogenetics. Because of its faster photocycle compared to wild-type (WT) ChR2, the E123T mutant of ChR2 is a useful optogenetic tool when fast neuronal stimulation is needed. Interestingly, in spite of its faster photocycle, the initial step of the photocycle in E123T (photoisomerization of retinal protonated Schiff base or RPSB) was found experimentally to be much slower than that of WT ChR2. The E123T mutant replaces the negatively charged E123 residue with a neutral T123 residue, perturbing the electric field around the RPSB. Understanding the RPSB photoisomerization mechanism in ChR2 mutants will provide molecular-level insights into how ChR2 photochemical reactivity can be controlled, which will lay the foundation for improving the design of optogenetic tools. In this work, we combine ab initio nonadiabatic dynamics simulation, excited state free energy calculation, and reaction path search to comprehensively characterize the RPSB photoisomerization mechanism in the E123T mutant of ChR2. Our simulation agrees with previous experiments in predicting a red-shifted absorption spectrum and significant slowdown of photoisomerization in the E123T mutant. Interestingly, our simulations predict similar photoisomerization quantum yields for the mutant and WT despite the differences in excited-state lifetime and absorption maximum. Upon mutation, the neutralization of the negative charge on the E123 residue increases the isomerization barrier, alters the reaction pathway, and changes the relative stability of two fluorescent states. Our findings provide new insight into the intricate role of the electrostatic environment on the RPSB photoisomerization mechanism in microbial rhodopsins.

Frontiers in Multiscale Modeling of Photoreceptor Proteins

This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments.

Intermolecular conical intersections in molecular aggregates

Conical intersections (CoIns) of multidimensional potential energy surfaces are ubiquitous in nature and control pathways and yields of many photo-initiated intramolecular processes. Such topologies can be potentially involved in the energy transport in aggregated molecules or polymers but are yet to be uncovered. Here, using ultrafast two-dimensional electronic spectroscopy (2DES), we reveal the existence of intermolecular CoIns in molecular aggregates relevant for photovoltaics. Ultrafast, sub-10-fs 2DES tracks the coherent motion of a vibrational wave packet on an optically bright state and its abrupt transition into a dark state via a CoIn after only 40 fs. Non-adiabatic dynamics simulations identify an intermolecular CoIn as the source of these unusual dynamics. Our results indicate that intermolecular CoIns may effectively steer energy pathways in functional nanostructures for optoelectronics.

Fluorescence Anisotropy Detection of Barrier Crossing and Ultrafast Conformational Dynamics in the S2 State of β-Carotene

Carotenoids are usually only weakly fluorescent despite being very strong absorbers in the mid-visible region because their first two excited singlet states, S₁ and S₂, have very short lifetimes. To probe the structural mechanisms that promote the nonradiative decay of the S₂ state to the S₁ state, we have carried out a series of fluorescence lineshape and anisotropy measurements with a prototype carotenoid, β-carotene, in four aprotic solvents. The anisotropy values observed in the fluorescence emission bands originating from the S₂ and S₁ states reveal that the large internal rotations of the emission transition dipole moment, as much as 50° relative to that of the absorption transition dipole moment, are initiated during ultrafast evolution on the S₂ state potential energy surface and persist upon nonradiative decay to the S₁ state. Electronic structure calculations of the orientation of the transition dipole moment account for the anisotropy results in terms of torsional and pyramidal distortions near the center of the isoprenoid backbone. The excitation wavelength dependence of the fluorescence anisotropy indicates that these out-of-plane conformational motions are initiated by passage over a low-activation energy barrier from the Franck-Condon S₂ structure. This conclusion is consistent with detection over the 80-200 K range of a broad, red-shifted fluorescence band from a dynamic intermediate evolving on a steep gradient of the S₂ state potential energy surface after crossing the activation barrier. The temperature dependence of the oscillator strength and anisotropy indicate that nonadiabatic passage from S₂ through a conical intersection seam to S₁ is promoted by the out-of-plane motions of the isoprenoid backbone with strong hindrance by solvent friction.

Quantum and Quantum-Classical Studies of the Photoisomerization of a Retinal Chromophore Model

We report an in-depth analysis of the photo-induced isomerization of the 2-cis-penta-2,4-dieniminium cation: a minimal model of the 11-cis retinal protonated Schiff base chromophore of the dim-light photoreceptor rhodopsin. Based on recently developed three-dimensional potentials parametrized on ab initio multi-state multi-configurational second-order perturbation theory data, we perform quantum-dynamical studies. In addition, simulations based on various quantum-classical methods, among which Tully surface hopping and the coupled-trajectory approach derived from the exact factorization, allow us to validate their performance against vibronic wavepacket propagation and, therefore, a purely quantum treatment. Quantum-dynamics results uncover qualitative differences with respect to the two-dimensional Hahn-Stock potentials, widely used as model potentials for the isomerization of the same chromophore, due to the increased dimensionality and three-mode correlation. Quantum-classical simulations show, instead, that three-dimensional model potentials are capable of capturing a number of features revealed by atomistic simulations and experimental observations. In particular, a recently reported vibrational phase relationship between double-bond torsion and hydrogen-out-of-plane modes critical for rhodopsin isomerization efficiency is correctly reproduced.

A systematic model study quantifying how conical intersection topography modulates photochemical reactions

Despite their important role in photochemistry and expected presence in most polyatomic molecules, conical intersections have been thoroughly characterized in a comparatively small number of systems. Conical intersections can confer molecular photoreactivity or photostability, often with remarkable efficacy, due to their unique structure: at a conical intersection, the adiabatic potential energy surfaces of two or more electronic states are degenerate, enabling ultrafast decay from an excited state without radiative emission, known as nonadiabatic transfer. Furthermore, the precise conical intersection topography determines fundamental properties of photochemical processes, including excited-state decay rate, efficacy, and molecular products that are formed. However, these relationships have yet to be defined comprehensively. In this article, we use an adaptable computational model to investigate a variety of conical intersection topographies, simulate resulting nonadiabatic dynamics, and calculate key photochemical observables. We varied the vibrational mode frequencies to modify conical intersection topography systematically in four primary classes of conical intersections and quantified the resulting rate, total yield, and product yield of nonadiabatic decay. The results reveal that higher vibrational mode frequencies reduce nonadiabatic transfer, but increase the transfer rate and resulting photoproduct formation. These trends can inform progress toward experimental control of photochemical reactions or tuning of molecules' photochemical properties based on conical intersections and their topography.

Dual Photoisomerization on Distinct Potential Energy Surfaces in a UV-Absorbing Rhodopsin

UV-absorbing rhodopsins are essential for UV vision and sensing in all kingdoms of life. Unlike the well-known visible-absorbing rhodopsins, which bind a protonated retinal Schiff base for light absorption, UV-absorbing rhodopsins bind an unprotonated retinal Schiff base. Thus far, the photoreaction dynamics and mechanisms of UV-absorbing rhodopsins have remained essentially unknown. Here, we report the complete excited- and ground-state dynamics of the UV form of histidine kinase rhodopsin 1 (HKR1) from eukaryotic algae, using femtosecond stimulated Raman spectroscopy (FSRS) and transient absorption spectroscopy, covering time scales from femtoseconds to milliseconds. We found that energy-level ordering is inverted with respect to visible-absorbing rhodopsins, with an optically forbidden low-lying S₁ excited state that has Ag^– symmetry and a higher-lying UV-absorbing S₂ state of Bu⁺ symmetry. UV-photoexcitation to the S₂ state elicits a unique dual-isomerization reaction: first, C13=C14 cis–trans isomerization occurs during S₂–S₁ evolution in <100 fs. This very fast reaction features the remarkable property that the newly formed isomer appears in the excited state rather than in the ground state. Second, C15=N16 anti–syn isomerization occurs on the S₁–S₀ evolution to the ground state in 4.8 ps. We detected two ground-state unprotonated retinal photoproducts, 13-trans/15-anti (all-trans) and 13-cis/15-syn, after relaxation to the ground state. These isomers become protonated in 58 μs and 3.2 ms, respectively, resulting in formation of the blue-absorbing form of HKR1. Our results constitute a benchmark of UV-induced photochemistry of animal and microbial rhodopsins.

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

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

Multistate Multiconfiguration Quantum Chemical Computation of the Two-Photon Absorption Spectra of Bovine Rhodopsin

Recently, progress in IR sources has led to the discovery that humans can detect infrared (IR) light. This is hypothesized to be due to the two-photon absorption (TPA) events promoting the retina dim-light rod photoreceptor rhodopsin to the same excited state populated via one-photon absorption (OPA). Here, we combine quantum mechanics/molecular mechanics and extended multiconfiguration quasi-degenerate perturbation theory calculations to simulate the TPA spectrum of bovine rhodopsin (Rh) as a model for the human photoreceptor. The results show that the TPA spectrum of Rh has an intense S₀ → S₁ band but shows also S₀ → S₂ and S₀ → S₃ transitions whose intensities, relative to the S₀ → S₁ band, are significantly increased when compared to the corresponding bands of the OPA spectrum. In conclusion, we show that IR light in the 950 nm region can be perceived by rod photoreceptors, thus supporting the two-photon origin of the IR perception. We also found that the same photoreceptor can perceive red (i.e., close to 680 nm) light provided that TPA induces population of S₂.

Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins

Computational chemistry provides versatile methods for studying the properties and functioning of biological systems at different levels of precision and at different time scales. The aim of this article is to review the computational methodologies that are applicable to rhodopsins as archetypes for photoactive membrane proteins that are of great importance both in nature and in modern technologies. For each class of computational techniques, from methods that use quantum mechanics for simulating rhodopsin photophysics to less-accurate coarse-grained methodologies used for long-scale protein dynamics, we consider possible applications and the main directions for improvement.

A molecular movie of ultrafast singlet fission

The complex dynamics of ultrafast photoinduced reactions are governed by their evolution along vibronically coupled potential energy surfaces. It is now often possible to identify such processes, but a detailed depiction of the crucial nuclear degrees of freedom involved typically remains elusive. Here, combining excited-state time-domain Raman spectroscopy and tree-tensor network state simulations, we construct the full 108-atom molecular movie of ultrafast singlet fission in a pentacene dimer, explicitly treating 252 vibrational modes on 5 electronic states. We assign the tuning and coupling modes, quantifying their relative intensities and contributions, and demonstrate how these modes coherently synchronise to drive the reaction. Our combined experimental and theoretical approach reveals the atomic-scale singlet fission mechanism and can be generalized to other ultrafast photoinduced reactions in complex systems. This will enable mechanistic insight on a detailed structural level, with the ultimate aim to rationally design molecules to maximise the efficiency of photoinduced reactions.

Conical Intersections at the Nanoscale: Molecular Ideas for Materials

The ability to predict and describe nonradiative processes in molecules via the identification and characterization of conical intersections is one of the greatest recent successes of theoretical chemistry. Only recently, however, has this concept been extended to materials science, where nonradiative recombination limits the efficiencies of materials for various optoelectronic applications. In this review, we present recent advances in the theoretical study of conical intersections in semiconductor nanomaterials. After briefly introducing conical intersections, we argue that specific defects in materials can induce conical intersections between the ground and first excited electronic states, thus introducing pathways for nonradiative recombination. We present recent developments in theoretical methods, computational tools, and chemical intuition for the prediction of such defect-induced conical intersections. Through examples in various nanomaterials, we illustrate the significance of conical intersections for nanoscience. We also discuss challenges facing research in this area and opportunities for progress.

A QM/MM study of the initial excited state dynamics of green-absorbing proteorhodopsin

The primary photochemical reaction of the green-absorbing proteorhodopsin is studied by means of a hybrid quantum mechanics/molecular mechanics (QM/MM) approach. The simulations are based on a homology model derived from the blue-absorbing proteorhodopsin crystal structure. The geometry of retinal and the surrounding sidechains in the protein binding pocket were optimized using the QM/MM method. Starting from this geometry the isomerization was studied with a relaxed scan along the C13[double bond, length as m-dash]C14 dihedral. It revealed an "aborted bicycle pedal" mechanism of isomerization that was originally proposed by Warshel for bovine rhodopsin and bacteriorhodopsin. However, the isomerization involved the concerted rotation about C13[double bond, length as m-dash]C14 and C15[double bond, length as m-dash]N, with the latter being highly twisted but not isomerized. Further, the simulation showed an increased steric interaction between the hydrogen at the C14 of the isomerizing bond and the hydroxyl group at the neighbouring tyrosine 200. In addition, we have simulated a nonadiabatic trajectory which showed the timing of the isomerization. In the first 20 fs upon excitation the order of the conjugated double and single bonds is inverted, consecutively the C13[double bond, length as m-dash]C14 rotation is activated for 200 fs until the S1-S0 transition is detected. However, the isomerization is reverted due to the specific interaction with the tyrosine as observed along the relaxed scan calculation. Our simulations indicate that the retinal - tyrosine 200 interaction plays an important role in the outcome of the photoisomerization.

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.

Intrinsic photoisomerization dynamics of protonated Schiff-base retinal

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

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

Mapping the ultrafast vibrational dynamics of all-trans and 13-cis retinal isomerization in Anabaena Sensory Rhodopsin

Discrepancies in the isomerization dynamics and quantum yields of the trans and cis retinal protonated Schiff base is a well-known issue in the context of retinal photochemistry. Anabaena Sensory Rhodopsin (ASR) is a microbial retinal protein that comprises a retinal chromophore in two ground state (GS) conformations: all-trans, 15-anti (AT) and 13-cis, 15-syn (13C). In this study, we applied impulsive vibrational spectroscopic techniques (DFWM, pump-DFWM and pump-IVS) to ASR to shed more light on how the structural changes take place in the excited state within the same protein environment. Our findings point to distinct features in the ground state structural conformations as well as to drastically different evolutions in the excited state manifold. The ground state vibrational spectra show stronger Raman activity of the C14-H out-of-plane wag (at about 805 cm-1) for the 13C isomer than that for the AT isomer, which hints at a pre-distortion of 13C in the ground state. Evolution of the Raman frequency after interaction with the actinic pulse shows a blue-shift for the C[double bond, length as m-dash]C stretching and CH3 rocking mode for both isomers. For AT, however, the blue-shift is not instantaneous as observed for the 13C isomer, rather it takes more than 200 fs to reach the maximum frequency shift. This frequency blue-shift is rationalized by a decrease in the effective conjugation length during the isomerization reaction, which further confirms a slower formation of the twisted state for the AT isomer and corroborates the presence of a barrier in the excited state trajectory previously predicted by quantum chemical calculations.

Insight into the chromophore of rhodopsin and its Meta-II photointermediate by 19F solid-state NMR and chemical shift tensor calculations

19F nuclei are useful labels in solid-state NMR studies, since their chemical shift and tensor elements are very sensitive to the electrostatic and space-filling properties of their local environment. In this study we have exploited a fluorine substituent, strategically placed at the C-12-position of 11-cis retinal, the chromophore of visual rhodopsins. This label was used to explore the local environment of the chromophore in the ground state of bovine rhodopsin and its active photo-intermediate Meta II. In addition, the chemical shift and tensor elements of the chromophore in the free state in a membrane environment and the bound state in the protein were determined. Upon binding of the chromophore into rhodopsin and Meta II, the isotropic chemical shift changes in the opposite direction by +9.7 and -8.4 ppm, respectively. An unusually large isotropic shift difference of 35.9 ppm was observed between rhodopsin and Meta II. This partly originates in the light-triggered 11-cis to all-trans isomerization of the chromophore. The other part reflects the local conformational rearrangements in the chromophore and the binding pocket. These NMR data were correlated with the available X-ray structures of rhodopsin and Meta II using bond polarization theory. For this purpose hydrogen atoms have to be inserted and hereto a family of structures were derived that best correlated with the well-established 13C chemical shifts. Based upon these structures, a 12-F derivative was obtained that best corresponded with the experimentally determined 19F chemical shifts and tensor elements. The combined data indicate strong changes in the local environment of the C-12 position and a substantially different interaction pattern with the protein in Meta II as compared to rhodopsin.

Relationship between Excited State Lifetime and Isomerization Quantum Yield in Animal Rhodopsins: Beyond the One-Dimensional Landau-Zener Model

We show that the speed of the chromophore photoisomerization of animal rhodopsins is not a relevant control knob for their light sensitivity. This result is at odds with the momentum-driven tunnelling rationale (i.e., assuming a one-dimensional Landau-Zener model for the decay: Zener, C. Non-Adiabatic Crossing of Energy Levels. Proc. R. Soc. London, Ser. A 1932, 137 (833), 696-702) holding that a faster nuclear motion through the conical intersection translates into a higher quantum yield and, thus, light sensitivity. Instead, a model based on the phase-matching of specific excited state vibrational modes should be considered. Using extensive semiclassical hybrid quantum mechanics/molecular mechanics trajectory computations to simulate the photoisomerization of three animal rhodopsin models (visual rhodopsin, squid rhodopsin and human melanopsin), we also demonstrate that phase-matching between three different modes (the reactive carbon and hydrogen twisting coordinates and the bond length alternation mode) is required to achieve high quantum yields. In fact, such "phase-matching" mechanism explains the computational results and provides a tool for the prediction of the photoisomerization outcome in retinal proteins.

Photoinduced processes in nucleic acids and proteins: concluding remarks

Light induced charge and energy transport in nucleic acids and proteins is the basis of fundamental biological processes such as photosynthesis, vision, DNA-photostability, DNA-photodamage and photosensing. This article summarises the concluding remarks given at the Faraday Discussions meeting on this topic. The specific themes arising from the meeting that are discussed herein include charge transfer in nucleic acids and proteins, excited state dynamics and topology, vibrations and dynamic disorder, proteins and charge transfer states, nanobiophotonics coupled to biomedical applications and photosynthesis.

How Methylation Modifies the Photophysics of the Native All- trans-Retinal Protonated Schiff Base: A CASPT2/MD Study in Gas Phase and in Methanol

A comparison between the free-energy surfaces of the all- trans-retinal protonated Schiff base (RPSB) and its 10-methylated derivative in gas phase and methanol solution is performed at CASSCF//CASSCF and CASPT2//CASSCF levels. Solvent effects were included using the average solvent electrostatic potential from molecular dynamics method. This is a QM/MM (quantum mechanics/molecular mechanics) method that makes use of the mean field approximation. It is found that the methyl group bonded to C10 produces noticeable changes in the solution free-energy profile of the S₁ excited state, mainly in the relative stability of the minimum energy conical intersections (MECIs) with respect to the Franck-Condon (FC) point. The conical intersections yielding the 9- cis and 11- cis isomers are stabilized while that yielding the 13- cis isomer is destabilized; in fact, it becomes inaccessible by excitation to S₁. Furthermore, the planar S₁ minimum is not present in the methylated compound. The solvent notably stabilizes the S₂ excited state at the FC geometry. Therefore, if the S₂ state has an effect on the photoisomerization dynamics, it must be because it permits the RPSB population to branch around the FC point. All these changes combine to speed up the photoisomerization in the 10-methylated compound with respect to the native compound.

Photoprotection: extending lessons learned from studying natural sunscreens to the design of artificial sunscreen constituents

Evolution has ensured that plants and animals have developed effective protection mechanisms against the potentially harmful effects of incident ultraviolet radiation (UVR). Tanning is one such mechanism in humans, but tanning only occurs post-exposure to UVR. Hence, there is ever growing use of commercial sunscreens to pre-empt overexposure to UVR. Key requirements for any chemical filter molecule used in such a photoprotective capacity include a large absorption cross-section in the UV-A and UV-B spectral regions and the availability of one or more mechanisms whereby the absorbed photon energy can be dissipated without loss of the molecular integrity of the chemical filter. Here we summarise recent experimental (mostly ultrafast pump-probe spectroscopy studies) and computational progress towards unravelling various excited state decay mechanisms that afford the necessary photostability in chemical filters found in nature and those used in commercial sunscreens. We also outline ways in which a better understanding of the photophysics and photochemistry of sunscreen molecules selected by nature could aid the design of new and improved commercial sunscreen formulations.

Excitation spectra of retinal by multiconfiguration pair-density functional theory

Retinal is the chromophore in proteins responsible for vision. The absorption maximum of retinal is sensitive to mutations of the protein. However, it is not easy to predict the absorption spectrum of retinal accurately, and questions remain even after intensive investigation. Retinal poses a challenge for Kohn-Sham density functional theory (KS-DFT) because of the charge transfer character in its excitations, and it poses a challenge for wave function theory because the large size of the molecule makes multiconfigurational perturbation theory methods expensive. In this study, we demonstrate that multiconfiguration pair-density functional theory (MC-PDFT) provides an efficient way to predict the vertical excitation energies of 11-Z retinal, and it reproduces the experimentally determined absorption band widths and peak positions better than complete active space second-order perturbation theory (CASPT2). The consistency between complete active space self-consistent field (CASSCF) and KS-DFT dipole moments is demonstrated to be a useful criterion in selecting the active space. We also found that the nature of the terminal groups and the conformations of retinal play a significant role in the absorption spectrum. By considering a thermal distribution of conformations, we predict an absorption spectrum of retinal that is consistent with the experimental gas-phase spectrum. The location of the absorption peak and the spectral broadening based on MC-PDFT calculations agree better with experiments than those of CASPT2.

Engineering the vibrational coherence of vision into a synthetic molecular device

The light-induced double-bond isomerization of the visual pigment rhodopsin operates a molecular-level optomechanical energy transduction, which triggers a crucial protein structure change. In fact, rhodopsin isomerization occurs according to a unique, ultrafast mechanism that preserves mode-specific vibrational coherence all the way from the reactant excited state to the primary photoproduct ground state. The engineering of such an energy-funnelling function in synthetic compounds would pave the way towards biomimetic molecular machines capable of achieving optimum light-to-mechanical energy conversion. Here we use resonance and off-resonance vibrational coherence spectroscopy to demonstrate that a rhodopsin-like isomerization operates in a biomimetic molecular switch in solution. Furthermore, by using quantum chemical simulations, we show why the observed coherent nuclear motion critically depends on minor chemical modifications capable to induce specific geometric and electronic effects. This finding provides a strategy for engineering vibrationally coherent motions in other synthetic systems.

The ultrafast, vibrationally coherent photoisomerization of rhodopsin is a model of efficient photomechanical energy conversion at the molecular scale. Here, the authors demonstrate a similar photoreaction in synthetic compounds, unraveling the underlying mechanism and discussing its implications.