Photochemical reaction dynamics of the primary event of vision studied by means of a hybrid molecular simulation

Tracking nuclear wave packets in excited-state reactions via quantum mechanics/molecular dynamics simulations

Nuclear wave packets (NWPs) in electronically excited states generated by ultrashort laser pulses can persist through photochemical processes and be detected in the product state. The NWPs that are coupled with the reaction dynamics undergo changes during the process and provide crucial insights into potential energy surfaces and molecular reaction dynamics. We present a computational method to calculate NWPs in the products of ultrafast photochemical processes by projecting nuclear displacements, obtained via Born-Oppenheimer molecular dynamics simulations, onto the normal modes of the reaction product state. Applying this approach to the excited-state intramolecular proton transfer reaction of 10-hydroxybenzo[h]quinoline, we successfully reproduced the experimentally observed NWPs in the reaction product, which were measured by time-resolved fluorescence of the product state with high fidelity. This significant achievement enables the analysis of individual normal mode motions following photoexcitation in chemical and physical processes. By integrating highly time-resolved spectroscopy with computational modeling, this method provides an effective approach to investigate the excited-state potential energy surfaces and the associated nuclear dynamics.

Investigation of the Nonradiative Photoprocesses of Unnatural DNA Base: 7-(2-Thienyl)-imidazo[4,5-b]pyridine (Ds)─A Computational Study

7-(2-Thienyl)-imidazo[4,5-b]pyridine (Ds) is an unnatural nucleic acid that forms a stable pair with pyrrole-2-carbaldehyde (Pa) in DNA. This Ds-Pa pair gets stabilized via van der Waals interaction and shape fitting. In our previous study [Ghosh, P. J. Phys. Chem. A 2021, 125, 5556-5561], we investigated the nonradiative photoprocesses of the unnatural DNA base Pa, and also there are some studies on its stability and reactivity in the ground state. But, to consider it as a good unnatural base pair, one has to understand its stability not only in the ground state but also in the excited states after absorbing ultraviolet (UV) radiation. Therefore, in this study, the excited-state photoprocesses of Ds on UV irradiation and its nonradiative decay channels have been investigated using state-of-the-art multireference methods, and this investigation finally leads the molecule to access the minimum energy crossing point (MECP) via a downhill pathway.

Exploring the Mechanisms behind Non-aromatic Fluorescence with the Density Functional Tight Binding Method

Recent experimental findings reveal nonconventional fluorescence emission in biological systems devoid of conjugated bonds or aromatic compounds, termed non-aromatic fluorescence (NAF). This phenomenon is exclusive to aggregated or solid states and remains absent in monomeric solutions. Previous studies focused on small model systems in vacuum show that the carbonyl stretching mode along with strong interaction of short hydrogen bonds (SHBs) remains the primary vibrational mode explaining NAF in these systems. In order to simulate larger model systems taking into account the effects of the surrounding environment, in this work we propose using the density functional tight-binding (DFTB) method in combination with non-adiabatic molecular dynamics (NAMD) and the mixed quantum/molecular mechanics (QM/MM) approach. We investigate the mechanism behind NAF in the crystal structure of l-pyroglutamine-ammonium, comparing it with the related nonfluorescent amino acid l-glutamine. Our results extend our previous findings to more realistic systems, demonstrating the efficiency and robustness of the proposed DFTB method in the context of NAMD in biological systems. Furthermore, due to its inherent low computational cost, this method allows for a better sampling of the nonradiative events at the conical intersection which is crucial for a complete understanding of this phenomenon. Beyond contributing to the ongoing exploration of NAF, this work paves the way for future application of this method in more complex biological systems such as amyloid aggregates, biomaterials, and non-aromatic proteins.

Recommendations for Velocity Adjustment in Surface Hopping

This study investigates velocity adjustment directions after hopping in surface hopping dynamics. Using fulvene and a protonated Schiff base (PSB4) as case studies, we investigate the population decay and reaction yields of different sets of dynamics with the velocity adjusted in either the nonadiabatic coupling, gradient difference, or momentum directions. For the latter, in addition to the conventional algorithm, we investigated the performance of a reduced kinetic energy reservoir approach recently proposed. Our evaluation also considered velocity adjustment in the directions of approximate nonadiabatic coupling vectors. While results for fulvene are susceptible to the adjustment approach, PSB4 is not. We correlated this dependence to the topography near the conical intersections. When nonadiabatic coupling vectors are unavailable, the gradient difference direction is the best adjustment option. If the gradient difference is also unavailable, a semiempirical vector direction or the momentum direction with a reduced kinetic energy reservoir becomes an excellent option to prevent an artificial excess of back hoppings. The precise velocity adjustment direction is less crucial for describing the nonadiabatic dynamics than the kinetic energy reservoir's size.

Unique Vibrational Characteristics and Structures of the Photoexcited Retinal Chromophore in Ion-Pumping Rhodopsins

Photoisomerization of an all-trans-retinal chromophore triggers ion transport in microbial ion-pumping rhodopsins. Understanding chromophore structures in the electronically excited (S1) state provides insights into the structural evolution on the potential energy surface of the photoexcited state. In this study, we examined the structure of the S1-state chromophore in Natronomonas pharaonis halorhodopsin (NpHR), a chloride ion-pumping rhodopsin, using time-resolved resonance Raman spectroscopy. The spectral patterns of the S1-state chromophore were completely different from those of the ground-state chromophore, resulting from unique vibrational characteristics and the structure of the S1 state. Mode assignments were based on a combination of deuteration shifts of the Raman bands and hybrid quantum mechanics-molecular mechanics calculations. The present observations suggest a weakened bond alternation in the π conjugation system. A strong hydrogen-out-of-plane bending band was observed in the Raman spectra of the S1-state chromophore in NpHR, indicating a twisted polyene structure. Similar frequency shifts for the C═N/C═C and C-C stretching modes of the S1-state chromophore in NpHR were observed in the Raman spectra of sodium ion-pumping and proton-pumping rhodopsins, suggesting that these unique features are common to the S1 states of ion-pumping rhodopsins.

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.

Humidity-Controlled Molecular Assembly and Photoisomerization Behavior with a Bubble-Assisted Patterning Approach

Precise control of molecular assembly is of great significance in the application of functional molecules. This work has systematically investigated the humidity effect in bubble-assisted molecular assembly. This work finds humidity is critical in the evolution of the soft confined space, leading to the formation of microscale liquid confined space under high humidity, and nanoscale liquid confined space under low humidity. It is also revealed that the differences in surface wettability and adhesion play the key role. Consequently, a flat pattern with thermodynamically favorable ordered structure and a sharp pattern with dynamically favorable disordered structure are achieved, which show different solid-state photoisomerization behaviors and photoresponsiveness. Interestingly, conductivity of sharp pattern with disordered structure is higher than that of flat pattern with layered ordered structure due to electronic transport mechanism of different spatial dimensions. This work opens a new way for manipulating the molecular self-assembly to control the morphology and function of molecular patterns.

Structural Impact of Selected Retinoids on Model Photoreceptor Membranes

Photoreceptor membranes have a unique lipid composition. They contain a high level of polyunsaturated fatty acids including the most unsaturated fatty acid in nature, docosahexaenoic acid (22:6), and are enriched in phosphatidylethanolamines. The phospholipid composition and cholesterol content of the subcellular components of photoreceptor outer segments enables to divide photoreceptor membranes into three types: plasma membranes, young disc membranes, and old disc membranes. A high degree of lipid unsaturation, extended exposure to intensive irradiation, and high respiratory demands make these membranes sensitive to oxidative stress and lipid peroxidation. Moreover, all-trans retinal (AtRAL), which is a photoreactive product of visual pigment bleaching, accumulates transiently inside these membranes, where its concentration may reach a phototoxic level. An elevated concentration of AtRAL leads to accelerated formation and accumulation of bisretinoid condensation products such as A2E or AtRAL dimers. However, a possible structural impact of these retinoids on the photoreceptor-membrane properties has not yet been studied. In this work we focused just on this aspect. The changes induced by retinoids, although noticeable, seem not to be significant enough to be physiologically relevant. This is, however, an positive conclusion because it can be assumed that accumulation of AtRAL in photoreceptor membranes will not affect the transduction of visual signals and will not disturb the interaction of proteins engaged in this process.

Nonadiabatic Coupling in Trajectory Surface Hopping: How Approximations Impact Excited-State Reaction Dynamics

Photochemical reactions are widely modeled using the popular trajectory surface hopping (TSH) method, an affordable mixed quantum-classical approximation to the full quantum dynamics of the system. TSH is able to account for nonadiabatic effects using an ensemble of trajectories, which are propagated on a single potential energy surface at a time and which can hop from one electronic state to another. The occurrences and locations of these hops are typically determined using the nonadiabatic coupling between electronic states, which can be assessed in a number of ways. In this work, we benchmark the impact of some approximations to the coupling term on the TSH dynamics for several typical isomerization and ring-opening reactions. We have identified that two of the schemes tested, the popular local diabatization scheme and a scheme based on biorthonormal wave function overlap implemented in the OpenMOLCAS code as part of this work, reproduce at a much reduced cost the dynamics obtained using the explicitly calculated nonadiabatic coupling vectors. The other two schemes tested can give different results, and in some cases, even entirely incorrect dynamics. Of these two, the scheme based on configuration interaction vectors gives unpredictable failures, while the other scheme based on the Baeck-An approximation systematically overestimates hopping to the ground state as compared to the reference approaches.

Quantum and semiclassical dynamical studies of nonadiabatic processes in solution: achievements and perspectives

We concisely review the main methodological approaches to model nonadiabatic dynamics in isotropic solutions and their applications. Three general classes of models are identified as the most used to include solvent effects in the simulations. The first model describes the solvent as a set of harmonic collective modes coupled to the solute degrees of freedom, and the second as a continuum, while the third explicitly includes solvent molecules in the calculations. The issues related to the use of these models in semiclassical and quantum dynamical simulations are discussed, as well as the main limitations and perspectives of each approach.

Multifaceted aspects of charge transfer

Charge transfer and charge transport are by far among the most important processes for sustaining life on Earth and for making our modern ways of living possible. Involving multiple electron-transfer steps, photosynthesis and cellular respiration have been principally responsible for managing the energy flow in the biosphere of our planet since the Great Oxygen Event. It is impossible to imagine living organisms without charge transport mediated by ion channels, or electron and proton transfer mediated by redox enzymes. Concurrently, transfer and transport of electrons and holes drive the functionalities of electronic and photonic devices that are intricate for our lives. While fueling advances in engineering, charge-transfer science has established itself as an important independent field, originating from physical chemistry and chemical physics, focusing on paradigms from biology, and gaining momentum from solar-energy research. Here, we review the fundamental concepts of charge transfer, and outline its core role in a broad range of unrelated fields, such as medicine, environmental science, catalysis, electronics and photonics. The ubiquitous nature of dipoles, for example, sets demands on deepening the understanding of how localized electric fields affect charge transfer. Charge-transfer electrets, thus, prove important for advancing the field and for interfacing fundamental science with engineering. Synergy between the vastly different aspects of charge-transfer science sets the stage for the broad global impacts that the advances in this field have.

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.

Nuclear-electronic all-particle density matrix renormalization group

We introduce the Nuclear-Electronic All-Particle Density Matrix Renormalization Group (NEAP-DMRG) method for solving the time-independent Schrödinger equation simultaneously for electrons and other quantum species. In contrast to the already existing multicomponent approaches, in this work, we construct from the outset a multi-reference trial wave function with stochastically optimized non-orthogonal Gaussian orbitals. By iterative refining of the Gaussians' positions and widths, we obtain a compact multi-reference expansion for the multicomponent wave function. We extend the DMRG algorithm to multicomponent wave functions to take into account inter- and intra-species correlation effects. The efficient parameterization of the total wave function as a matrix product state allows NEAP-DMRG to accurately approximate the full configuration interaction energies of molecular systems with more than three nuclei and 12 particles in total, which is currently a major challenge for other multicomponent approaches. We present the NEAP-DMRG results for two few-body systems, i.e., H₂ and H₃ ⁺, and one larger system, namely, BH₃.

Multiscale Molecular Modeling in G Protein-Coupled Receptor (GPCR)-Ligand Studies

G protein-coupled receptors (GPCRs) are major drug targets due to their ability to facilitate signal transduction across cell membranes, a process that is vital for many physiological functions to occur. The development of computational technology provides modern tools that permit accurate studies of the structures and properties of large chemical systems, such as enzymes and GPCRs, at the molecular level. The advent of multiscale molecular modeling permits the implementation of multiple levels of theories on a system of interest, for instance, assigning chemically relevant regions to high quantum mechanics (QM) level of theory while treating the rest of the system using classical force field (molecular mechanics (MM) potential). Multiscale QM/MM molecular modeling have far-reaching applications in the rational design of GPCR drugs/ligands by affording precise ligand binding configurations through the consideration of conformational plasticity. This enables the identification of key binding site residues that could be targeted to manipulate GPCR function. This review will focus on recent applications of multiscale QM/MM molecular simulations in GPCR studies that could boost the efficiency of future structure-based drug design (SBDD) strategies.

Observe while it happens: catching photoactive proteins in the act with non-adiabatic molecular dynamics simulations

Organisms use photo-receptors to react to light. The first step is usually the absorption of a photon by a prosthetic group embedded inside the photo-receptor, often a conjugated chromophore. The electronic changes in the chromophore induced by photo-absorption can trigger a cascade of structural or chemical transformations that culminate into a response to light. Understanding how these proteins have evolved to mediate their activation process has remained challenging because the required time and spacial resolutions are notoriously difficult to achieve experimentally. Therefore, mechanistic insights into photoreceptor activation have been predominantly obtained with computer simulations. Here we briefly outline the challenges associated with such computations and review the progress made in this field.

Molecular Dynamics of Excited State Intramolecular Charge Transfer in Solution by Coherent Nuclear Wave Packets

Revealing a proper reaction coordinate in a chemical reaction is the key step towards elucidation of the molecular reaction dynamics. In this report, we investigated the dynamics of intramolecular charge transfer (ICT) of 8-aminopyrene-1,3,6-trisulfonic acid (APTS) occurring in the excited state by time-resolved fluorescence (TF) and TF spectra. Accurate reaction rates and rate-dependent nuclear wave packets in the product state allow detailed investigation of the molecular reaction dynamics. The ICT rate is solvent dependent: (34 fs)^-1 , (87 fs)^-1 , and (∞)^-1 in water, formamide, and dimethylformamide, respectively. By recording spectra of the nuclear wave packets for different reaction rates, chemical species responsible for the emission spectra can be positively identified. The origin of the wave packets can be deduced from the amplitude change of the wave packets at different reaction rates, and the vibrational modes that are associated with the reaction coordinate could be identified. Theoretical calculations of the vibrational reorganization energies reproduce the experimental spectrum of the nuclear wave packets and corroborate the conclusions.

Ligand Binding Mechanisms in Human Cone Visual Pigments

Vertebrate vision starts with light absorption by visual pigments in rod and cone photoreceptor cells of the retina. Rhodopsin, in rod cells, responds to dim light, whereas three types of cone opsins (red, green, and blue) function under bright light and mediate color vision. Cone opsins regenerate with retinal much faster than rhodopsin, but the molecular mechanism of regeneration is still unclear. Recent advances in the area pinpoint transient intermediate opsin conformations, and a possible secondary retinal-binding site, as determinant factors for regeneration. In this Review, we compile previous and recent findings to discuss possible mechanisms of ligand entry in cone opsins, involving a secondary binding site, which may have relevant functional and evolutionary implications.

An Atomistic Model of a Precursor State of Light-Induced Channel Opening of Channelrhodopsin

Channelrhodopsins (ChRs) are microbial light-gated ion channels with a retinal chromophore and are widely utilized in optogenetics to precisely control neuronal activity with light. Despite increasing understanding of their structures and photoactivation kinetics, the atomistic mechanism of light gating and ion conduction remains elusive. Here, we present an atomic structural model of a chimeric ChR in a precursor state of the channel opening determined by an accurate hybrid molecular simulation technique and a statistical theory of internal water distribution. The photoactivated structure features extensive tilt of the chromophore accompanied by redistribution of water molecules in its binding pocket, which is absent in previously known photoactivated structures of analogous photoreceptors, and widely agrees with structural and spectroscopic experimental evidence of ChRs. The atomistic model manifests a photoactivated ion-conduction pathway that is markedly different from a previously proposed one and successfully explains experimentally observed mutagenic effects on key channel properties.

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.

Photoactivation Intermediates of a G-Protein Coupled Receptor Rhodopsin Investigated by a Hybrid Molecular Simulation

Rhodopsin is a G-protein coupled receptor functioning as a photoreceptor for vision through photoactivation of a covalently bound ligand of a retinal protonated Schiff base chromophore. Despite the availability of structural information on the inactivated and activated forms of the receptor, the transition processes initiated by the photoabsorption have not been well understood. Here we theoretically examined the photoactivation processes by means of molecular dynamics (MD) simulations and ab initio quantum mechanical/molecular mechanical (QM/MM) free energy geometry optimizations which enabled accurate geometry determination of the ligand molecule in ample statistical conformational samples of the protein. Structures of the intermediate states of the activation process, blue-shifted intermediate and Lumi, as well as the dark state first generated by MD simulations and then refined by the QM/MM free energy geometry optimizations were characterized by large displacement of the β-ionone ring of retinal along with change in the hydrogen bond of the protonated Schiff base. The ab initio calculations of vibrational and electronic spectroscopic properties of those states well reproduced the experimental observations and successfully identified the molecular origins underlying the spectroscopic features. The structural evolution in the formation of the intermediates provides a molecular insight into the efficient activation processes of the receptor.

Theoretical description of protein field effects on electronic excitations of biological chromophores

Photoinitiated phenomena play a crucial role in many living organisms. Plants, algae, and bacteria absorb sunlight to perform photosynthesis, and convert water and carbon dioxide into molecular oxygen and carbohydrates, thus forming the basis for life on Earth. The vision of vertebrates is accomplished in the eye by a protein called rhodopsin, which upon photon absorption performs an ultrafast isomerisation of the retinal chromophore, triggering the signal cascade. Many other biological functions start with the photoexcitation of a protein-embedded pigment, followed by complex processes comprising, for example, electron or excitation energy transfer in photosynthetic complexes. The optical properties of chromophores in living systems are strongly dependent on the interaction with the surrounding environment (nearby protein residues, membrane, water), and the complexity of such interplay is, in most cases, at the origin of the functional diversity of the photoactive proteins. The specific interactions with the environment often lead to a significant shift of the chromophore excitation energies, compared with their absorption in solution or gas phase. The investigation of the optical response of chromophores is generally not straightforward, from both experimental and theoretical standpoints; this is due to the difficulty in understanding diverse behaviours and effects, occurring at different scales, with a single technique. In particular, the role played by ab initio calculations in assisting and guiding experiments, as well as in understanding the physics of photoactive proteins, is fundamental. At the same time, owing to the large size of the systems, more approximate strategies which take into account the environmental effects on the absorption spectra are also of paramount importance. Here we review the recent advances in the first-principle description of electronic and optical properties of biological chromophores embedded in a protein environment. We show their applications on paradigmatic systems, such as the light-harvesting complexes, rhodopsin and green fluorescent protein, emphasising the theoretical frameworks which are of common use in solid state physics, and emerging as promising tools for biomolecular systems.

Femtosecond spectroscopic study of photochromic reactions of bacteriorhodopsin and visual rhodopsin

Photochromic ultrafast reactions of bacteriorhodopsin (H. salinarum) and bovine rhodopsin were conducted with a femtosecond two-pump probe pulse setup with the time resolution of 20-25fs. The dynamics of the forward and reverse photochemical reactions for both retinal-containing proteins was compared. It is demonstrated that when retinal-containing proteins are excited by femtosecond pulses, dynamics pattern of the vibrational coherent wave packets in the course of the reaction is different for bacteriorhodopsin and visual rhodopsin. As shown in these studies, the low-frequencies that form a wave packets experimentally observed in the dynamics of primary products formation as a result of retinal photoisomerization have different intensities and are clearer for bovine rhodopsin. Photo-reversible reactions for both retinal proteins were performed from the stage of the relatively stable photointermediates that appear within 3-5ps after the light pulse impact. It is demonstrated that the efficiency of the reverse phototransition K-form→bacteriorhodopsin is almost five-fold higher than that of the Batho-intermediate→visual rhodopsin phototransition. The results obtained indicate that in the course of evolution the intramolecular mechanism of the chromophore-protein interaction in visual rhodopsin becomes more perfect and specific. The decrease in the probability of the reverse chromophore photoisomerization (all-trans→11-cis retinal) in primary photo-induced rhodopsin products causes an increase in the efficiency of the photoreception process.

Quantum-Classical Nonadiabatic Dynamics: Coupled- vs Independent-Trajectory Methods

Trajectory-based mixed quantum-classical approaches to coupled electron-nuclear dynamics suffer from well-studied problems such as the lack of (or incorrect account for) decoherence in the trajectory surface hopping method and the inability of reproducing the spatial splitting of a nuclear wave packet in Ehrenfest-like dynamics. In the context of electronic nonadiabatic processes, these problems can result in wrong predictions for quantum populations and in unphysical outcomes for the nuclear dynamics. In this paper, we propose a solution to these issues by approximating the coupled electronic and nuclear equations within the framework of the exact factorization of the electron-nuclear wave function. We present a simple quantum-classical scheme based on coupled classical trajectories and test it against the full quantum mechanical solution from wave packet dynamics for some model situations which represent particularly challenging problems for the above-mentioned traditional methods.

Competitive excited-state single or double proton transfer mechanisms for bis-2,5-(2-benzoxazolyl)-hydroquinone and its derivatives

The excited state intramolecular proton transfer (ESIPT) mechanisms of 2-(2-hydroxyphenyl)benzoxazole (HBO), bis-2,5-(2-benzoxazolyl)-hydroquinone (BBHQ) and 2,5-bis(5'-tert-butyl-benzoxazol-2'-yl)hydroquinone (DHBO) have been investigated using time-dependent density functional theory (TDDFT). The calculated vertical excitation energies based on the TDDFT method reproduced the experimental absorption and emission spectra well. Three kinds of stable structures were found on the S1 state potential energy surface (PES). A new ESIPT mechanism that differs from the one proposed previously (Mordzinski et al., Chem. Phys. Lett., 1983, 101, 291. and Lim et al., J. Am. Chem. Soc., 2006, 128, 14542.) is proposed. The new mechanism includes the possibility of simultaneous double proton transfer, or successive single transfers, in addition to the accepted single proton transfer mechanism. Hydrogen bond strengthening in the excited state was based on primary bond lengths, angles, IR vibrational spectra and hydrogen bond energy. Intramolecular charge transfer based on the frontier molecular orbitals (MOs) also supports the proposed mechanism of the ESIPT reaction. To further elucidate the proposed mechanism, reduced dimensionality PESs of the S0 and S1 states were constructed by keeping the O-H distance fixed at a series of values. The potential barrier heights among the local minima on the S1 surface imply competitive single and double proton transfer branches in the mechanism. Based on the new ESIPT mechanism, the observed fluorescence quenching can be satisfactorily explained.

Effect of amino group on the excited-state intramolecular proton transfer (ESIPT) mechanisms of 2-(2′-hydroxyphenyl)benzoxazole and its amino derivatives

The electronic density redistributes and it migrates in opposite directions for HBO when compared to those of 5A-HBO and 6A-HBO. The amino group in the HBO framework can change the behavior of the intramolecular hydrogen bonds.

Coupled-Trajectory Quantum-Classical Approach to Electronic Decoherence in Nonadiabatic Processes

We present a novel quantum-classical approach to nonadiabatic dynamics, deduced from the coupled electronic and nuclear equations in the framework of the exact factorization of the electron-nuclear wave function. The method is based on the quasiclassical interpretation of the nuclear wave function, whose phase is related to the classical momentum and whose density is represented in terms of classical trajectories. In this approximation, electronic decoherence is naturally induced as an effect of the coupling to the nuclei and correctly reproduces the expected quantum behavior. Moreover, the splitting of the nuclear wave packet is captured as a consequence of the correct approximation of the time-dependent potential of the theory. This new approach offers a clear improvement over Ehrenfest-like dynamics. The theoretical derivation presented in this Letter is supported by numerical results that are compared to quantum mechanical calculations.

The exact forces on classical nuclei in non-adiabatic charge transfer

The decomposition of electronic and nuclear motion presented in Abedi et al. [Phys. Rev. Lett. 105, 123002 (2010)] yields a time-dependent potential that drives the nuclear motion and fully accounts for the coupling to the electronic subsystem. Here, we show that propagation of an ensemble of independent classical nuclear trajectories on this exact potential yields dynamics that are essentially indistinguishable from the exact quantum dynamics for a model non-adiabatic charge transfer problem. We point out the importance of step and bump features in the exact potential that are critical in obtaining the correct splitting of the quasiclassical nuclear wave packet in space after it passes through an avoided crossing between two Born-Oppenheimer surfaces and analyze their structure. Finally, an analysis of the exact potentials in the context of trajectory surface hopping is presented, including preliminary investigations of velocity-adjustment and the force-induced decoherence effect.

New excited-state proton transfer mechanisms for 1,8-dihydroxydibenzo[a,h]phenazine

The excited state intramolecular proton transfer (ESIPT) mechanisms of 1,8-dihydroxydibenzo[a,h]phenazine (DHBP) in toluene solvent have been investigated based on time-dependent density functional theory (TD-DFT). The results suggest that both a single and double proton transfer mechanisms are relevant, in constrast to the prediction of a single one proposed previously (Piechowska et al. J. Phys. Chem. A 2014, 118, 144-151). The calculated results show that the intramolecular hydrogen bonds were formed in the S0 state, and upon excitation, the intramolecular hydrogen bonds between -OH group and pyridine-type nitrogen atom would be strengthened in the S1 state, which can facilitate the proton transfer process effectively. The calculated vertical excitation energies in the S0 and S1 states reproduce the experimental UV-vis absorption and fluorescence spectra well. The constructed potential energy surfaces of the S0 and S1 states have been used to explain the proton transfer process. Four minima have been found on the S1 state surface, with potential barriers between these excited-state minima of less than 10 kcal/mol, which supports concomitant single and double proton transfer mechanisms. In addition, the fluorescence quenching can be explained reasonably based on the proton transfer process.

Shape of Multireference, Equation-of-Motion Coupled-Cluster, and Density Functional Theory Potential Energy Surfaces at a Conical Intersection

We report and characterize ground-state and excited-state potential energy profiles using a variety of electronic structure methods along a loop lying on the branching plane associated with a conical intersection (CI) of a reduced retinal model, the penta-2,4-dieniminium cation (PSB3). Whereas the performance of the equation-of-motion coupled-cluster, density functional theory, and multireference methods had been tested along the excited- and ground-state paths of PSB3 in our earlier work, the ability of these methods to correctly describe the potential energy surface shape along a CI branching plane has not yet been investigated. This is the focus of the present contribution. We find, in agreement with earlier studies by others, that standard time-dependent DFT (TDDFT) does not yield the correct two-dimensional (i.e., conical) crossing along the branching plane but rather a one-dimensional (i.e., linear) crossing along the same plane. The same type of behavior is found for SS-CASPT2(IPEA=0), SS-CASPT2(IPEA=0.25), spin-projected SF-TDDFT, EOM-SF-CCSD, and, finally, for the reference MRCISD+Q method. In contrast, we found that MRCISD, CASSCF, MS-CASPT2(IPEA=0), MS-CASPT2(IPEA=0.25), XMCQDPT2, QD-NEVPT2, non-spin-projected SF-TDDFT, and SI-SA-REKS yield the expected conical crossing. To assess the effect of the different crossing topologies (i.e., linear or conical) on the PSB3 photoisomerization efficiency, we discuss the results of 100 semiclassical trajectories computed by CASSCF and SS-CASPT2(IPEA=0.25) for a PSB3 derivative. We show that for the same initial conditions, the two methods yield similar dynamics leading to isomerization quantum yields that differ by only a few percent.

Retinal ligand mobility explains internal hydration and reconciles active rhodopsin structures

Rhodopsin, the mammalian dim-light receptor, is one of the best-characterized G-protein-coupled receptors, a pharmaceutically important class of membrane proteins that has garnered a great deal of attention because of the recent availability of structural information. Yet the mechanism of rhodopsin activation is not fully understood. Here, we use microsecond-scale all-atom molecular dynamics simulations, validated by solid-state (2)H nuclear magnetic resonance spectroscopy, to understand the transition between the dark and metarhodopsin I (Meta I) states. Our analysis of these simulations reveals striking differences in ligand flexibility between the two states. Retinal is much more dynamic in Meta I, adopting an elongated conformation similar to that seen in the recent activelike crystal structures. Surprisingly, this elongation corresponds to both a dramatic influx of bulk water into the hydrophobic core of the protein and a concerted transition in the highly conserved Trp265(6.48) residue. In addition, enhanced ligand flexibility upon light activation provides an explanation for the different retinal orientations observed in X-ray crystal structures of active rhodopsin.

QM/MM investigations of organic chemistry oriented questions

About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar strategy.