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

The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry

The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations

Probing the Photochemistry of Rhodopsin Through Population Dynamics Simulations

The primary event in vision is induced by the ultrafast photoisomerization of rhodopsin, the dim-light visual pigment of vertebrates. While spectroscopic and theoretical studies have identified certain vibrationally coherent atomic motions to promote the rhodopsin photoisomerization, how exactly and to what degree such coherence is biologically related with its isomerizing efficiency (i.e. the photoisomerization quantum yield) remains unknown. In fact, in the past, the computational cost limited the simulation of the rhodopsin photoisomerization dynamics, which could be carried out only for a single molecule or a small set of molecules, therefore lacking the necessary statistical description of a molecular population motion. In this Dissertation I apply a hybrid quantum mechanics/molecular mechanics (QM/MM) models of bovine rhodopsin, the verterbrate visual pigment, to tackle the basic issues mentioned above. Accordingly, my work has been developing along three different lines comprising the development, testing and application of new tools for population dynamics simulation: (I) Development of a suitable protocol to investigate the excited state population dynamics of rhodopsins at room temperature. (II) A correlation between the phase of a hydrogen-out-of-plane (HOOP) motion at the decay point and the outcome of the rhodopsin photoisomerization. (III) A population “splitting” mechanism adopted by the protein to maximize its quantum yield and, therefore, light sensitivity. In conclusion, my Dissertation reports, for the first time, a connection between the initial coherent motion of a population of rhodopsin molecules and the quantum efficiency of their isomerization. The photoisomerization efficiency is ultimately determined by the way in which the degree of coherence of the excited state population motion is modulated by the protein sequence and conformation

Probing the Photochemistry of Rhodopsin Through Population Dynamics Simulations

The primary event in vision is induced by the ultrafast photoisomerization of rhodopsin, the dim-light visual pigment of vertebrates. While spectroscopic and theoretical studies have identified certain vibrationally coherent atomic motions to promote the rhodopsin photoisomerization, how exactly and to what degree such coherence is biologically related with its isomerizing efficiency (i.e. the photoisomerization quantum yield) remains unknown. In fact, in the past, the computational cost limited the simulation of the rhodopsin photoisomerization dynamics, which could be carried out only for a single molecule or a small set of molecules, therefore lacking the necessary statistical description of a molecular population motion. In this Dissertation I apply a hybrid quantum mechanics/molecular mechanics (QM/MM) models of bovine rhodopsin, the verterbrate visual pigment, to tackle the basic issues mentioned above. Accordingly, my work has been developing along three different lines comprising the development, testing and application of new tools for population dynamics simulation: (I) Development of a suitable protocol to investigate the excited state population dynamics of rhodopsins at room temperature. (II) A correlation between the phase of a hydrogen-out-of-plane (HOOP) motion at the decay point and the outcome of the rhodopsin photoisomerization. (III) A population “splitting” mechanism adopted by the protein to maximize its quantum yield and, therefore, light sensitivity. In conclusion, my Dissertation reports, for the first time, a connection between the initial coherent motion of a population of rhodopsin molecules and the quantum efficiency of their isomerization. The photoisomerization efficiency is ultimately determined by the way in which the degree of coherence of the excited state population motion is modulated by the protein sequence and conformation

Electronic State Mixing Controls the Photoreactivity of a Rhodopsin with all- trans Chromophore Analogues

Rhodopsins hosting synthetic retinal protonated Schiff base analogues are important for developing tools for optogenetics and high-resolution imaging. The ideal spectroscopic properties of such analogues include long-wavelength absorption/emission and fast/hindered photoisomerization. While the former may be achieved, for instance, by elongating the chromophore π-system, the latter requires a detailed understanding of the substituent effects (i.e., steric or electronic) on the chromophore light-induced dynamics. In the present letter we compare the results of quantum mechanics/molecular mechanics excited-state trajectories of native and analogue-hosting microbial rhodopsins from the eubacterium Anabaena. The results uncover a relationship between the nature of the substituent on the analogue (i.e., electron-donating (a Me group) or electron-withdrawing (a CF3 group)) and rhodopsin excited-state lifetime. Most importantly, we show that electron-donating or -withdrawing substituents cause a decrease or an increase in the electronic mixing of the first two excited states which, in turn, controls the photoisomerization speed

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. The 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 that 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 of quantum efficiency and, therefore, biomimetic behavior

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 -C13C14- rotation of microbial rhodopsins while the second channel is characterized by the -C11C12- rotation typical of animal rhodopsins. The fact that such -C11C12- 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

Localization and Frequency Identification of Large-Range Wide-Band Electromagnetic Interference Sources in Electromagnetic Imaging System

The identification and localization of large-range, wide-band electromagnetic interference (EMI) sources have always been both costly and time-consuming. The measurements at different times and places are often required before a typical system can locate a target. In this paper, we proposed a 2D electromagnetic imaging system to localize interference sources and identify the EMI frequency in real time. In this system, an offset paraboloid with a diameter of three meters is designed for large-range EMI imaging, while a multi-channel digital signal acquisition system is developed for wide-band EMI localization. The located interference source is segmented by the maximum entropy method based on particle swarm optimization, and the modified generalized regression neural network (MGRNN) is applied to identify the EMI frequency effectively by excluding misleading effects of outliers. The experiment which has been completed on our dataset indicates that our approach not only increases accuracy by 5% compared with the standard generalized regression neural network approaches for identification, but also exerts a large-range wide-band localization of the EMI source detection method