Picosecond quantum-classical dynamics reveals that the coexistence of light-induced microbial and animal chromophore rotary motion modulates the isomerization quantum yield of heliorhodopsin.

Rhodopsins are light-responsive proteins forming two vast and evolutionary distinct superfamilies whose functions are invariably triggered by the photoisomerization of a single retinal chromophore. In 2018 a third widespread superfamily of rhodopsins called heliorhodopsins was discovered using functional metagenomics. Heliorhodopsins, with their markedly different structural features with respect to the animal and microbial superfamilies, offer an opportunity to study how evolution has manipulated the chromophore photoisomerization to achieve adaptation. One question is related to the mechanism of such a reaction and how it differs from that of animal and microbial rhodopsins. To address this question, we use hundreds of quantum-classical trajectories to simulate the spectroscopically documented picosecond light-induced dynamics of a heliorhodopsin from the archaea thermoplasmatales archaeon (TaHeR). We show that, consistently with the observations, the trajectories reveal two excited state decay channels. However, inconsistently with previous hypotheses, only one channel is associated with the -C13C14- rotation of microbial rhodopsins while the second channel is characterized by the -C11C12- rotation typical of animal rhodopsins. The fact that such -C11C12- rotation is aborted upon decay and ground state relaxation, explains why illumination of TaHeR only produces the 13-cis isomer with a low quantum efficiency. We argue that the documented lack of regioselectivity in double-bond excited state twisting motion is the result of an "adaptation" that could be completely lost via specific residue substitutions modulating the steric hindrance experienced along the isomerization motion.

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

Correction for 'From a one-mode to a multi-mode understanding of conical intersection mediated ultrafast organic photochemical reactions' by Yorrick Boeije et al., Chem. Soc. Rev., 2023, 52, 2643-2687, https://doi.org/10.1039/D2CS00719C.

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

Over the last few decades, conical intersections (CoIns) have grown from theoretical curiosities into common mechanistic features of photochemical reactions, whose function is to funnel electronically excited molecules back to their ground state in regions where the potential energy surfaces (PESs) of two electronic states become degenerate. Analogous to transition states in thermal chemistry, CoIns appear as transient structures providing a kinetic bottleneck along a reaction coordinate. However, such a bottleneck is not associated with the probability of crossing an energy barrier but rather with an excited state decay probability along a full "line" of transient structures connected by non-reactive modes, the intersection space (IS). This article will review our understanding of the factors controlling CoIn mediated ultrafast photochemical reactions, taking a physical organic chemist approach by discussing a number of case studies for small organic molecules and photoactive proteins. Such discussion will be carried out by first introducing the "standard" one-mode model based on Landau-Zener (LZ) theory to describe a reactive excited state decay event intercepting, locally, a single CoIn along a single direction, and then by providing a modern perspective based on the effects of the phase matching of multiple modes on the same local event, thus redefining and expanding the description of the excited state reaction coordinate. The direct proportionality between the slope (or velocity) along one mode and decay probability at a single CoIn is a widely applied fundamental principle that follows from the LZ model, yet it fails to provide a complete understanding of photochemical reactions whose local reaction coordinate changes along the IS. We show that in these situations, in particular by focussing on rhodopsin double bond photoisomerization, it is mandatory to consider additional molecular modes and their phase relationship approaching the IS, hence providing a key mechanistic principle of ultrafast photochemistry based on the phase matching of those modes. We anticipate that this qualitative mechanistic principle should be considered in the rational design of any ultrafast excited state process, impacting various fields of research ranging from photobiology to light-driven molecular devices.

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.

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.

Design, Synthesis and Characterization of a Visible-Light-Sensitive Molecular Switch and Its PEGylation Towards a Self-Assembling Molecule.

HBDI-like chromophores represent a novel set of biomimetic switches mimicking the fluorophore of the green fluorescent protein that are currently studied with the hope to expand the molecular switch/motor toolbox. However, until now members capable of absorbing visible light in their neutral (i. e. non-anionic) form have not been reported. In this contribution we report the preparation of an HBDI-like chromophore based on a 3-phenylbenzofulvene scaffold capable of absorbing blue light and photoisomerizing on the picosecond timescale. More specifically, we show that double-bond photoisomerization occurs in both the E-to-Z and Z-to-E directions and that these can be controlled by irradiating with blue and UV light, respectively. Finally, as a preliminary applicative result, we report the incorporation of the chromophore in an amphiphilic molecule and demonstrate the formation of a visible-light-sensitive nanoaggregated state in water.

Web-ARM: A Web-Based Interface for the Automatic Construction of QM/MM Models of Rhodopsins.

This article introduces Web-ARM, a specialized tool, online available, designed to build quantum mechanical/molecular mechanical models of rhodopsins, a widely spread family of light-responsive proteins. Web-ARM allows the rapidly building of models of rhodopsins with a documented quality and the prediction of trends in UV-vis absorption maximum wavelengths, based on their excitation energies computed at the CASPT2//CASSCF/Amber level of theory. Web-ARM builds upon the recently reported, python-based a-ARM protocol [J. Chem. Theory Comput., 2019, 15, 3134-3152] and, as such, necessitates only a crystallographic structure or a comparative model in PDB format and a very basic knowledge of the studied rhodopsin system. The user-friendly web interface uses such input to generate congruous, gas-phase models of rhodopsins and, if requested, their mutants. We present two possible applications of Web-ARM, which showcase how the interface can be employed to assist both research and educational activities in fields at the interface between chemistry and biology. The first application shows how, through Web-ARM, research projects (e.g., rhodopsin and rhodopsin mutant screening) can be carried out in significantly less time with respect to using the required computational photochemistry tools via a command line. The second application documents the use of Web-ARM in a real-life educational/training activity, through a hands-on experience illustrating the concepts of rhodopsin color tuning.

Modern quantum chemistry with [Open]Molcas.

MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.

Fluorescence Enhancement of a Microbial Rhodopsin via Electronic Reprogramming.

The engineering of microbial rhodopsins with enhanced fluorescence is of great importance in the expanding field of optogenetics. Here we report the discovery of two mutants (W76S/Y179F and L83Q) of a sensory rhodopsin from the cyanobacterium Anabaena PCC7120 with opposite fluorescence behavior. In fact, while W76S/Y179F displays, with respect to the wild-type protein, a nearly 10-fold increase in red-light emission, the second is not emissive. Thus, the W76S/Y179F, L83Q pair offers an unprecedented opportunity for the investigation of fluorescence enhancement in microbial rhodopsins, which is pursued by combining transient absorption spectroscopy and multiconfigurational quantum chemistry. The results of such an investigation point to an isomerization-blocking electronic effect as the direct cause of instantaneous (subpicosecond) fluorescence enhancement.

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[double bond, length as m-dash]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. All compounds undergo a sub-picosecond photoisomerization, and can be categorized within two photoisomerization scenarios. Scenario I corresponds to compounds which display the signatures of a vibrationally coherent reactive motion through the conical intersection, with different degrees of vibrational coherence. Qualitatively distinct TA signatures are observed for other compounds which are therefore proposed to obey scenario II, referring to an intermediate regime between scenario I and a thermally-equilibrated, fully stochastic photoreaction. Remarkably, the photoisomerization scenario is observed to correlate with the computed distortion from planarity of the ground state equilibrium geometry, reflecting the torsional strain that would be released after photoexcitation. The most planar compounds - i.e. those having a C[double bond, length as m-dash]C double bond pre-twist of less than 10° - obey scenario II, while compounds obeying scenario I have larger pre-twists. The most pre-twisted compounds (>15°) show pronounced oscillatory signatures of a reaction-induced, low-frequency vibrational wavepacket observed in the S0 photoproduct and assigned to the torsion mode of the reaction coordinate, thus mimicking the vibrationally coherent photoisomerization dynamics of the rhodopsin protein. Importantly, the systematic comparison of all photoisomerization quantum yields does however not reveal any correlation with observables such as excited state life time, vibrational coherence, absorption wavelengths or degree of pre-twisting.

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.

Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores.

Ultrafast processes in light-absorbing proteins have been implicated in the primary step in the light-to-energy conversion and the initialization of photoresponsive biological functions. Theory and computations have played an instrumental role in understanding the molecular mechanism of such processes, as they provide a molecular-level insight of structural and electronic changes at ultrafast time scales that often are very difficult or impossible to obtain from experiments alone. Among theoretical strategies, the application of hybrid quantum mechanics and molecular mechanics (QM/MM) models is an important approach that has reached an evident degree of maturity, resulting in several important contributions to the field. This review presents an overview of state-of-the-art computational studies on subnanosecond events in rhodopsins, photoactive yellow proteins, phytochromes, and some other photoresponsive proteins where photoinduced double-bond isomerization occurs. The review also discusses current limitations that need to be solved in future developments.

Two-State, Three-Mode Parametrization of the Force Field of a Retinal Chromophore Model.

In recent years, the potential energy surfaces of the penta-2,4-dieniminium cation have been investigated using several electronic structure methods. The resulting pool of geometrical, electronic, and energy data provides a suitable basis for the construction of a topographically correct analytical model of the molecule force field and, therefore, for a better understanding of this class of molecules, which includes the chromophore of visual pigments. In the present contribution, we report the construction of such a model for regions of the force field that drive the photochemical and thermal isomerization of the central double bound of the cation. While previous models included only two modes, it is here shown that the proposed three-mode model and corresponding set of parameters are able to reproduce the complex topographical and electronic structure features seen in electronically correlated data obtained at the XMCQDPT2//CASSCF/6-31G* level of theory.

Molecular bases for the selection of the chromophore of animal rhodopsins.

The functions of microbial and animal rhodopsins are triggered by the isomerization of their all-trans and 11-cis retinal chromophores, respectively. To lay the molecular basis driving the evolutionary transition from the all-trans to the 11-cis chromophore, multiconfigurational quantum chemistry is used to compare the isomerization mechanisms of the sensory rhodopsin from the cyanobacterium Anabaena PCC 7120 (ASR) and of the bovine rhodopsin (Rh). It is found that, despite their evolutionary distance, these eubacterial and vertebrate rhodopsins start to isomerize via distinct implementations of the same bicycle-pedal mechanism originally proposed by Warshel [Warshel A (1976) Nature 260:678-683]. However, by following the electronic structure changes of ASR (featuring the all-trans chromophore) during the isomerization, we find that ASR enters a region of degeneracy between the first and second excited states not found in Rh (featuring the 11-cis chromophore). We show that such degeneracy is modulated by the preorganized structure of the chromophore and by the position of the reactive double bond. It is argued that the optimization of the electronic properties of the chromophore, which affects the photoisomerization efficiency and the thermal isomerization barrier, provided a key factor for the emergence of the striking amino acid sequence divergence observed between the microbial and animal rhodopsins.

Comparison of the isomerization mechanisms of human melanopsin and invertebrate and vertebrate rhodopsins.

Comparative modeling and ab initio multiconfigurational quantum chemistry are combined to investigate the reactivity of the human nonvisual photoreceptor melanopsin. It is found that both the thermal and photochemical isomerization of the melanopsin 11-cis retinal chromophore occur via a space-saving mechanism involving the unidirectional, counterclockwise twisting of the =C11H-C12H= moiety with respect to its Lys340-linked frame as proposed by Warshel for visual pigments [Warshel A (1976) Nature 260(5553):679-683]. A comparison with the mechanisms documented for vertebrate (bovine) and invertebrate (squid) visual photoreceptors shows that such a mechanism is not affected by the diversity of the three chromophore cavities. Despite such invariance, trajectory computations indicate that although all receptors display less than 100 fs excited state dynamics, human melanopsin decays from the excited state ∼40 fs earlier than bovine rhodopsin. Some diversity is also found in the energy barriers controlling thermal isomerization. Human melanopsin features the highest computed barrier which appears to be ∼2.5 kcal mol(-1) higher than that of bovine rhodopsin. When assuming the validity of both the reaction speed/quantum yield correlation discussed by Warshel, Mathies and coworkers [Weiss RM, Warshel A (1979) J Am Chem Soc 101:6131-6133; Schoenlein RW, Peteanu LA, Mathies RA, Shank CV (1991) Science 254(5030):412-415] and of a relationship between thermal isomerization rate and thermal activation of the photocycle, melanopsin turns out to be a highly sensitive pigment consistent with the low number of melanopsin-containing cells found in the retina and with the extraretina location of melanopsin in nonmammalian vertebrates.

Optomechanical Control of Quantum Yield in Trans-Cis Ultrafast Photoisomerization of a Retinal Chromophore Model.

The quantum yield of a photochemical reaction is one of the most fundamental quantities in photochemistry, as it measures the efficiency of the transduction of light energy into chemical energy. Nature has evolved photoreceptors in which the reactivity of a chromophore is enhanced by its molecular environment to achieve high quantum yields. The retinal chromophore sterically constrained inside rhodopsin proteins represents an outstanding example of such a control. In a more general framework, mechanical forces acting on a molecular system can strongly modify its reactivity. Herein, we show that the exertion of tensile forces on a simplified retinal chromophore model provokes a substantial and regular increase in the trans-to-cis photoisomerization quantum yield in a counterintuitive way, as these extension forces facilitate the formation of the more compressed cis photoisomer. A rationale for the mechanochemical effect on this photoisomerization mechanism is also proposed.

Design, Synthesis, and Dynamics of a Green Fluorescent Protein Fluorophore Mimic with an Ultrafast Switching Function.

While rotary molecular switches based on neutral and cationic organic π-systems have been reported, structurally homologous anionic switches providing complementary properties have not been prepared so far. Here we report the design and preparation of a molecular switch mimicking the anionic p-HBDI chromophore of the green fluorescent protein. The investigation of the mechanism and dynamics of the E/Z switching function is carried out both computationally and experimentally. The data consistently support axial rotary motion occurring on a sub-picosecond time scale. Transient spectroscopy and trajectory simulations show that the nonadiabatic decay process occurs in the vicinity of a conical intersection (CInt) between a charge transfer state and a covalent/diradical state. Comparison of our anionic p-HBDI-like switch with the previously reported cationic N-alkyl indanylidene pyrrolinium switch mimicking visual pigments reveals that these similar systems translocate, upon vertical excitation, a similar net charge in the same axial direction.

Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table.

In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization.

Mechanism of excited state deactivation of indan-1-ylidene and fluoren-9-ylidene malononitriles.

Herein, we report complementary computational and experimental evidence supporting the existence, for indan-1-ylidene malononitrile and fluoren-9-ylidene malononitrile, of a non-radiative decay channel involving double bond isomerisation motion. The results of UV-Vis transient absorption spectroscopy highlight that the decay takes place within hundreds of picoseconds. In order to understand the related molecular mechanism, photochemical reaction paths were computed by employing multiconfigurational quantum chemistry. The results indicate that the excited state deactivation occurs via concerted double bond twisting of the dicyanovinyl (DCV) unit coupled with a pyramidalisation of its substituted carbon. It is also shown that the observed differences in the excited state lifetimes when passing from indan-1-ylidene malononitrile to fluoren-9-ylidene are associated with the change in the topography of the conical intersection driving the decay from intermediate to sloped, respectively.

A surface hopping algorithm for nonadiabatic minimum energy path calculations.

The article introduces a robust algorithm for the computation of minimum energy paths transiting along regions of near-to or degeneracy of adiabatic states. The method facilitates studies of excited state reactivity involving weakly avoided crossings and conical intersections. Based on the analysis of the change in the multiconfigurational wave function the algorithm takes the decision whether the optimization should continue following the same electronic state or switch to a different state. This algorithm helps to overcome convergence difficulties near degeneracies. The implementation in the MOLCAS quantum chemistry package is discussed. To demonstrate the utility of the proposed procedure four examples of application are provided: thymine, asulam, 1,2-dioxetane, and a three-double-bond model of the 11-cis-retinal protonated Schiff base.