Engineering the vibrational coherence of vision into a synthetic molecular device

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.

Automatic Rhodopsin Modeling with Multiple Protonation Microstates

Automatic Rhodopsin Modeling (ARM) is a simulation protocol providing QM/MM models of rhodopsins capable of reproducing experimental electronic absorption and emission trends. Currently, ARM is restricted to a single protonation microstate for each rhodopsin model. Herein, we incorporate an extension of the minimal electrostatic model (MEM) into the ARM protocol to account for all relevant protonation microstates at a given pH. The new ARM+MEM protocol determines the most important microstates contributing to the description of the absorption spectrum. As a test case, we have applied this methodology to simulate the pH-dependent absorption spectrum of a toy model, showing that the single-microstate picture breaks down at certain pH values. Subsequently, we applied ARM+MEM toAnabaenasensory rhodopsin, confirming an improved description of its absorption spectrum when the titration of several key residues is considered.

A visible-light-driven molecular motor based on barbituric acid

We present a class of visible-light-driven molecular motors based on barbituric acid. Due to a serendipitous reactivity we observed during their synthesis, these motors possess a tertiary stereogenic centre on the upper half, characterised by a hydroxy group. Using a combination of femto- and nanosecond transient absorption spectroscopy, molecular dynamics simulations and low-temperature 1H NMR experiments we found that these motors operate similarly to push-pull second-generation overcrowded alkene-based molecular motors. Interestingly, the hydroxy group at the stereocentre enables a hydrogen bond with the carbonyl groups of the barbituric acid lower half, which drives a sub-picosecond excited-state isomerisation, as observed spectroscopically. Computational simulations predict an excited state "lasso" mechanism where the intramolecular hydrogen bond pulls the molecule towards the formation of the metastable state, with a high predicted quantum yield of isomerisation (68%) in gas phase.

Investigation on Novel E/Z 2-Benzylideneindan-1-One-Based Photoswitches with AChE and MAO-B Dual Inhibitory Activity

The multitarget therapeutic strategy, as opposed to the more traditional 'one disease-one target-one drug', may hold promise in treating multifactorial neurodegenerative syndromes, such as Alzheimer's disease (AD) and related dementias. Recently, combining a photopharmacology approach with the multitarget-directed ligand (MTDL) design strategy, we disclosed a novel donepezil-like compound, namely 2-(4-((diethylamino)methyl)benzylidene)-5-methoxy-2,3-dihydro-1H-inden-1-one (1a), which in the E isomeric form (and about tenfold less in the UV-B photo-induced isomer Z) showed the best activity as dual inhibitor of the AD-related targets acetylcholinesterase (AChE) and monoamine oxidase B (MAO-B). Herein, we investigated further photoisomerizable 2-benzylideneindan-1-one analogs 1b-h with the unconjugated tertiary amino moiety bearing alkyls of different bulkiness and lipophilicity. For each compound, the thermal stable E geometric isomer, along with the E/Z mixture as produced by UV-B light irradiation in the photostationary state (PSS, 75% Z), was investigated for the inhibition of human ChEs and MAOs. The pure E-isomer of the N-benzyl(ethyl)amino analog 1h achieved low nanomolar AChE and high nanomolar MAO-B inhibition potencies (IC50s 39 and 355 nM, respectively), whereas photoisomerization to the Z isomer (75% Z in the PSS mixture) resulted in a decrease (about 30%) of AChE inhibitory potency, and not in the MAO-B one. Molecular docking studies were performed to rationalize the different E/Z selectivity of 1h toward the two target enzymes.

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.

Direct structural observation of ultrafast photoisomerization dynamics in sinapate esters

Sinapate esters have been extensively studied for their potential application in 'nature-inspired' photoprotection. There is general consensus that the relaxation mechanism of sinapate esters following photoexcitation with ultraviolet radiation is mediated by geometric isomerization. This has been largely inferred through indirect studies involving transient electronic absorption spectroscopy in conjunction with steady-state spectroscopies. However, to-date, there is no direct experimental evidence tracking the formation of the photoisomer in real-time. Using transient vibrational absorption spectroscopy, we report on the direct structural changes that occur upon photoexcitation, resulting in the photoisomer formation. Our mechanistic analysis predicts that, from the photoprepared ππ* state, internal conversion takes place through a conical intersection (CI) near the geometry of the initial isomer. Our calculations suggest that different CI topographies at relevant points on the seam of intersection may influence the isomerization yield. Altogether, we provide compelling evidence suggesting that a sinapate ester's geometric isomerization can be a more complex dynamical process than originally thought.

Xanthopsin-Like Systems via Site-Specific Click-Functionalization of a Retinoic Acid Binding Protein

The use of light-responsive proteins to control both living or synthetic cells, is at the core of the expanding fields of optogenetics and synthetic biology. It is thus apparent that a richer reaction toolbox for the preparation of such systems is of fundamental importance. Here, we provide a proof-of-principle demonstration that Morita-Baylis-Hillman adducts can be employed to perform a facile site-specific, irreversible and diastereoselective click-functionalization of a lysine residue buried into a lipophilic binding pocket and yielding an unnatural chromophore with an extended π-system. In doing so we effectively open the path to the in vitro preparation of a library of synthetic proteins structurally reminiscent of xanthopsin eubacterial photoreceptors. We argue that such a library, made of variable unnatural chromophores inserted in an easy-to-mutate and crystallize retinoic acid transporter, significantly expand the scope of the recently introduced rhodopsin mimics as both optogenetic and "lab-on-a-molecule" tools.

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.

Designing light-driven rotary molecular motors

The ability to induce and amplify motion at the molecular scale has seen tremendous progress ranging from simple molecular rotors to responsive materials. In the two decades since the discovery of light-driven rotary molecular motors, the development of these molecules has been extensive; moving from the realm of molecular chemistry to integration into dynamic molecular systems. They have been identified as actuators holding great potential to precisely control the dynamics of nanoscale devices, but integrating molecular motors effectively into evermore complex artificial molecular machinery is not trivial. Maximising efficiency without compromising function requires conscious and judicious selection of the structures used. In this perspective, we focus on the key aspects of motor design and discuss how to manipulate these properties without impeding motor integrity. Herein, we describe these principles in the context of molecular rotary motors featuring a central double bond axle and emphasise the strengths and weaknesses of each design, providing a comprehensive evaluation of all artificial light-driven rotary motor scaffolds currently present in the literature. Based on this discussion, we will explore the trajectory of research into the field of molecular motors in the coming years, including challenges to be addressed, potential applications, and future prospects.

Demystifying the Origin of Vibrational Coherence Transfer Between the S1 and T1 States of the Pt-pop Complex

We demonstrate that spin-vibronic coupling is the most significant mechanism in vibrational coherence transfer (VCT) from the singlet (S₁) to the triplet (T₁) state of the [Pt₂(P₂O₅H₂)₄]^4- complex. Our time-dependent correlation function-based study shows that the rate of intersystem crossing (k_ISC) through direct spin-orbit coupling is negligibly small, making VCT vanishingly small due to the ultrashort decoherence time (2.5 ps). However, the inclusion of the spin-vibronic contribution to the net k_ISC in selective normal modes along the Pt-Pt axis increases the k_ISC to such an extent that VCT becomes feasible. Our results suggest that k_ISC for the S₁ →T₂ (τ_ISC = 1.084 ps) is much faster than the S₁ → T₁ (τ_ISC = 763.4 ps) and S₁ → T₃ (τ_ISC = 13.38 ps) in CH₃CN solvent, indicating that VCT is possible from the low-lying excited singlet (S₁) to the triplet (T₁) state through the intermediate T₂ state. This is the first example where VCT occurs solely due to spin-vibronic interactions. This finding can pave the way for new types of photocatalysis.

Controlled ultrafast ππ*-πσ* dynamics in tryptophan-based peptides with tailored micro-environment

Ultrafast charge, energy and structural dynamics in molecules are driven by the topology of the multidimensional potential energy surfaces that determines the coordinated electronic and nuclear motion. These processes are also strongly influenced by the interaction with the molecular environment, making very challenging a general understanding of these dynamics on a microscopic level. Here we use electrospray and mass spectrometry technologies to produce isolated molecular ions with a controlled micro-environment. We measure ultrafast photo-induced ππ*-πσ* dynamics in tryptophan species in the presence of a single, charged adduct. A striking increase of the timescale by more than one order of magnitude is observed when changing the added adduct atom. A model is proposed to rationalize the results, based on the localized and delocalized effects of the adduct on the electronic structure of the molecule. These results offer perspectives to control ultrafast molecular processes by designing the micro-environment on the Angström length scale.

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.

On the Transition from a Biomimetic Molecular Switch to a Rotary Molecular Motor

The experimental investigation of the unidirectional motion characterizing the photoisomerization of single-molecule rotary motors requires accessible lab prototypes featuring an electronic circular dichroism (ECD) signal that is sensitive to the geometrical and electronic changes occurring during an ultrafast reactive process. Here we report a combined experimental/computational study of a candidate obtained via the asymmetrization of a light-driven biomimetic molecular switch. We show that the achieved motor has an ECD band that is remarkably sensitive to the isomerization motion, and it is therefore suitable for time-resolved ECD studies. However, we also find that, unexpectedly, the synthesized motor isomerizes on a time scale longer than the subpicosecond time measured for the achiral parent, a result that points to alternative candidates conserving a high reaction speed.

Lifetime Broadening and Impulsive Generation of Vibrational Coherence Triggered by Ultrafast Electron Transfer

The absorption band shape of chromophores in liquid solution at room temperature is usually dominated by pure electronic dephasing dynamics, which occurs on the sub-100 fs time scale. Herein, we report on a series of dyads consisting of a naphthalenediimide (NDI) electron acceptor with one or two phenyl-based donors for which photoinduced intramolecular electron transfer is fast enough to be competitive with pure electronic dephasing. As a consequence, the absorption band of the π-π* transition of these dyads is broader than that of the NDI alone to an extent that scales with the electron transfer rate. Additionally, this reaction is so fast that it leads to the impulsive excitation of a low-frequency vibrational mode of the charge-separated product. Quantum-chemical calculations suggest that this vibration involves the C-N donor-acceptor bond, which shortens considerably upon electron transfer.

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.

Nonadiabatic molecular dynamics simulation for the ultrafast photoisomerization of dMe-OMe-NAIP based on TDDFT on-the-fly potential energy surfaces

Global switching on-the-fly trajectory surface hopping molecular dynamics simulation was performed on the accurate TD-B3LYP/6-31G* potential energy surfaces for E-to-Z and Z-to-E photoisomerization of dMe-OMe-NAIP up to S1(ππ*) excitation. The present TD(DFT) simulation provides accurate calculation for conical intersections between the first-excited and ground states. Thus, simulated quantum yield and lifetime of 0.23 and 620 fs (0.15 and 600 fs) for E-to-Z (Z-to-E) isomerization are in good (relatively good) agreement with experimental observation of 0.25 and 480 fs (0.24 and 430 fs), respectively. Simulated results reveal that photoisomerization pathways are initially uphill to conical intersection zones on the S1 potential energy surface and then downhill to product zones. Three types of representative conical intersections are found for determining photoisomerization mechanisms: one is the rotation type responsible for reactive isomerization and the other two are close to E and Z configurations, respectively, only for nonreactive isomerization. The present conclusions can be held in general for similar large NAIP systems of photoinduced isomerization based on E and Z configurations.

Identification of Nonradiative Decay Pathways in Cy3

Photoexcited fluorescent markers are extensively used in spectroscopy, imaging, and analysis of biological systems. The performance of fluorescent markers depends on high levels of emission, which are limited by competing nonradiative decay pathways. Small-molecule fluorescent dyes have been increasingly used as markers due to their high and stable emission. Despite their prevalence, the nonradiative decay pathways of these dyes have not been determined. Here, we investigate these pathways for a widely used indocarbocyanine dye, Cy3, using transient grating spectroscopy. We identify a nonradiative decay pathway via a previously unknown dark state formed within ∼1 ps of photoexcitation. Our experiments, in combination with electronic structure calculations, suggest that the generation of the dark state is mediated by picosecond vibrational mode coupling, likely via a conical intersection. We further identify the vibrational modes, and thus structural elements, responsible for the formation and dynamics of the dark state, providing insight into suppressing nonradiative decay pathways in fluorescent markers such as Cy3.

Computational and Spectroscopic Characterization of the Photocycle of an Artificial Rhodopsin

The photocycle of a reversible photoisomerizing rhodopsin mimic (M2) is investigated. This system, based on the cellular retinoic acid binding protein, is structurally different from natural rhodopsin systems, but exhibits a similar isomerization upon light irradiation. More specifically, M2 displays a 15-cis to all-trans conversion of retinal protonated Schiff base (rPSB) and all-trans to 15-cis isomerization of unprotonated Schiff base (rUSB). Here we use hybrid quantum mechanics/molecular mechanics (QM/MM) tools coupled with transient absorption and cryokinetic UV-vis spectroscopies to investigate these isomerization processes. The results suggest that primary rPSB photoisomerization of M2 occurs around the C13═C14 double bond within 2 ps following an aborted-bicycle pedal (ABP) isomerization mechanism similar to natural microbial rhodopsins. The rUSB isomerization is much slower and occurs within 48 ps around the C15═N double bond. Our findings reveal the possibility to engineer naturally occurring mechanistic features into artificial rhodopsins and also constitute a step toward understanding the photoisomerization of UV pigments. We conclude by reinforcing the idea that the presence of the retinal chromophore inside a tight protein cavity is not mandatory to exhibit ABP mechanism.

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.

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.

Ultrafast photo-induced processes in complex systems require theoretical models and their experimental validation which are still lacking. Here the authors investigate singlet fission in a pentacene dimer by a combined experimental and theoretical approach providing a real-time visualisation of the process.

Synthesis, spectroscopy and QM/MM simulations of a biomimetic ultrafast light-driven molecular motor

A molecular motor potentially performing a continuous unidirectional rotation is studied by a multidisciplinary approach including organic synthesis, transient spectroscopy and excited state trajectory calculations. A stereogenic center was introduced in the N-alkylated indanylidene-pyrroline Schiff base framework of a previously investigated light-driven molecular switch in order to achieve the unidirectional C[double bond, length as m-dash]C rotary motion typical of Feringa's motor. Here we report that the specific substitution pattern of the designed chiral molecule must critically determine the unidirectional efficiency of the light-induced rotary motion. More specifically, we find that a stereogenic center containing a methyl group and a hydrogen atom as substituents does not create a differential steric effect large enough to fully direct the motion in either the clockwise or counterclockwise direction especially along the E→Z coordinate. However, due to the documented ultrafast character and electronic circular dichroism activity of the investigated system, we find that it provides the basis for development of a novel generation of rotary motors with a biomimetic framework and operating on a picosecond time scale.

E to Z Photoisomerization of Phytochrome Cph1Δ Exceeds the Born-Oppenheimer Adiabatic Limit

The Born-Oppenheimer adiabatic limit applies broadly in chemistry because most reactions occur on the ground electronic state. Photochemical reactions involve two or more electronic states and need not be subject to this adiabatic limit. The spectroscopic signatures of nonadiabatic processes are subtle, and therefore, experimental investigations have been limited to the few systems dominated by single photochemical outcomes. Systems with branched excited-state pathways have been neglected, despite their potential to reveal insights into photochemical reactivity. Here we present experimental evidence from coherent three-dimensional electronic spectroscopy that the E to Z photoisomerization of phytochrome Cph1 is strongly nonadiabatic, and the simulations reproduce the measured features only when the photoisomerization proceeds nonadiabatically near, but not through, a conical intersection. The results broaden the general understanding of photoisomerization mechanisms and motivate future studies of nonadiabatic processes with multiple outcomes arising from branching on excited-state potential energy surfaces.

a-ARM: Automatic Rhodopsin Modeling with Chromophore Cavity Generation, Ionization State Selection, and External Counterion Placement

The Automatic Rhodopsin Modeling (ARM) protocol has recently been proposed as a tool for the fast and parallel generation of basic hybrid quantum mechanics/molecular mechanics (QM/MM) models of wild type and mutant rhodopsins. However, in its present version, input preparation requires a few hours long user's manipulation of the template protein structure, which also impairs the reproducibility of the generated models. This limitation, which makes model building semiautomatic rather than fully automatic, comprises four tasks: definition of the retinal chromophore cavity, assignment of protonation states of the ionizable residues, neutralization of the protein with external counterions, and finally congruous generation of single or multiple mutations. In this work, we show that the automation of the original ARM protocol can be extended to a level suitable for performing the above tasks without user's manipulation and with an input preparation time of minutes. The new protocol, called a-ARM, delivers fully reproducible (i.e., user independent) rhodopsin QM/MM models as well as an improved model quality. More specifically, we show that the trend in vertical excitation energies observed for a set of 25 wild type and 14 mutant rhodopsins is predicted by the new protocol better than when using the original. Such an agreement is reflected by an estimated (relative to the probed set) trend deviation of 0.7 ± 0.5 kcal mol-1 (0.03 ± 0.02 eV) and mean absolute error of 1.0 kcal mol-1 (0.04 eV).

Bile Acid Binding Protein Functionalization Leads to a Fully Synthetic Rhodopsin Mimic

Rhodopsins are photoreceptive proteins using light to drive a plethora of biological functions such as vision, proton and ion pumping, cation and anion channeling, and gene and enzyme regulation. Here we combine organic synthesis, NMR structural studies, and photochemical characterization to show that it is possible to prepare a fully synthetic mimic of rhodopsin photoreceptors. More specifically, we conjugate a bile acid binding protein with a synthetic mimic of the rhodopsin protonated Schiff base chromophore to achieve a covalent complex featuring an unnatural protein host, photoswitch, and photoswitch-protein linkage with a reverse orientation. We show that, in spite of its molecular-level diversity, light irradiation of the prepared mimic fuels a photochromic cycle driven by sequential photochemical and thermal Z/E isomerizations reminiscent of the photocycles of microbial rhodopsins.

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.