Probing the Photodynamics of Rhodopsins with Reduced Retinal Chromophores

Manathunga, Madushanka; Yang, Xuchun; Luk, Hoi Ling; Gozem, Samer; Frutos, Luis Manuel; Valentini, Alessio; Ferré, Nicolas; Olivucci, Massimo

doi:10.1021/acs.jctc.5b00945

Cited by 53 publications

(61 citation statements)

References 41 publications

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“…The protonated Schiff base derivative of retinal is the chromophore involved in the vision process of seeing animals . The corresponding photoisomerization pathways of retinal, its Schiff base derivatives, and model compounds have been studied thoroughly by using multiconfigurational and multireference wavefunction methods . Gozem et al.…”

Section: Resultsmentioning

confidence: 99%

The Fractional Occupation Number Weighted Density as a Versatile Analysis Tool for Molecules with a Complicated Electronic Structure

Bauer

Hansen

Grimme

2017

Chemistry A European J

130

121

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The fractional occupation number weighted density (FOD) analysis is explored as a general theoretical diagnostic for complicated electronic structures. Its main feature is to provide robustly and quickly the information on the localization of "hot" (strongly correlated and chemically active) electrons in a molecule. We demonstrate its usage in four different prototypical applications: 1) As a new and fast measure of the biradical character of polycyclic aromatic hydrocarbons, 2) for the selection of active orbital spaces in multiconfigurational or complete active space self consistent field (MCSCF/CASSCF) treatments, 3) as a possibility to describe molecular-energy landscapes consistently in regions with varying biradical character, as exemplified by partial double-bond torsions, and 4) as a powerful visualization method for static electron correlation effects in large biomolecules in connection with an efficient semi-empirical tight-binding molecular orbital scheme. The last application opens a full quantum-mechanical, unbiased route to the automatic detection of errors in experimental protein X-ray structures, such as false protonation states or misplaced atoms. In the first example, the complete (unfragmented) quantum-chemical calculation of the FOD for an entire metalloprotein with more than 7500 atoms is described.

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Section: Resultsmentioning

confidence: 99%

The Fractional Occupation Number Weighted Density as a Versatile Analysis Tool for Molecules with a Complicated Electronic Structure

Bauer

Hansen

Grimme

2017

Chemistry A European J

130

121

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“…In the trajectories starting from M-Z11(S 0 ), the hops to the S 0 state through M-CI(S 1 S 0 )a re overwhelmingly dominant (blue in the left panel of Figure 2); in those starting from P-Z11(S 0 ), the hops through P-CI(S 1 S 0 ) dominate analogously (red in the right panel of Figure 2). In both cases,t he distribution of the hopping times shows an oscillatory pattern (bottom panel of Figure 2), which indicates that the approach to the conical intersection seam is modulated by ap eriodic structural change.T he average S 1 !S 0 hopping time is estimated to be around 50 fs.A periodic excited-state decay has also been seen in cis azobenzene and ar etinal chromophore model [17,37] but the stereospecific excited state decay is unique to Z11.…”

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confidence: 90%

Photoisomerization of Arylazopyrazole Photoswitches: Stereospecific Excited‐State Relaxation

Wang

Cui

et al. 2016

Angew Chem Int Ed

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Electronic structure calculations and nonadiabatic dynamics simulations (more than 2000 trajectories) are used to explore the Z-E photoisomerization mechanism and excitedstate decayd ynamics of two arylazopyrazole photoswitches. Tw oc hiral S 1 /S 0 conical intersections with associated enantiomeric S 1 relaxation paths that are barrierless and efficient (timescale of ca. 50 fs) were found. Forthe parent arylazopyrazole( Z8) both paths contribute evenly to the S 1 excited-state decay, whereas for the dimethyl derivative (Z11) each of the two chiral cis minima decays almost exclusively through one specific enantiomeric S 1 relaxation path. To our knowledge,the Z11 arylazopyrazole is thus the first example for nearly stereospecific unidirectional excited-state relaxation.Photoswitchable compounds have many potential applications ranging from photopharmacology through optochemical genetics to data storage. [1,2] Azobenzenes are among the most studied photoswitchable compounds,s ince they are easily synthesized and highly stable. [3,4] Their high extinction coefficients and isomerization quantum yields enable repeated photoswitching with low-intensity light. Photoinduced isomerization leads to ar emarkable change of the shape and length of these azobenzenes,w hich has been exploited, for example,intuning the folding and unfolding of peptides and proteins. [5][6][7][8] Many azobenzenes have been explored experimentally and computationally in the past decade, [9][10][11][12][13][14][15][16][17][18][19][20][21][22] but there remain af ew drawbacks that limit their broad application. These include incomplete photoswitching because of overlapping absorbance of the two isomers and fast thermal rearrangement of the cis isomer (Z)b ack to the trans isomer (E). To improve overall performance,many groups have explored the properties of azobenzene variants by altering the substituents on the aromatic rings,f or example,i nb ridged and orthohydroxy azobenzenes. [23][24][25][26][27][28][29][30] Recently,n ovel classes of azoheterocycle photoswitches were reported, [31][32][33][34][35][36] especially arylazopyrazoles,w hich provide quantitative photoswitching and high thermal stability (ca. 1000 days). [35,36] Thea bsorption band maxima of the Eand Z-isomers of arylazopyrazoles are found to be well separated, which enables quantitative two-way photoswitching.[35] Furthermore,t he substitution on the heterocyclic ring offers photophysical and photochemical properties that cannot be accessed with azobenzenes.H owever,t he photoinduced isomerization mechanism and the dynamical behavior of these arylazopyrazoles are still unexplored at the atomistic level. Obvious questions that remain are: 1) Whether azobenzenes and arylazopyrazoles share similar photophysical and photochemical mechanisms and 2) whether they show analogous dynamical behavior (lifetimes,c onical intersections,p ath selectivities). Ad etailed mechanistic understanding will be helpful to further improve their performance through rational design. Motivated by ...

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“…However, in several cases, the necessity to go beyond a purely static description of the PES is crucial to achieve a good comprehension of photophysics, especially when taking place in complex environments such as biological media. 25,26 Indeed, not only the environment may dramatically alter the PES, but the coupling between the chromophore and the environment degrees of freedom (i.e. the dynamics effects) may open totally new photophysical pathways.…”

mentioning

confidence: 99%

The effect of solvent relaxation in the ultrafast time-resolved spectroscopy of solvated benzophenone

Zvereva

Segarra‐Martí

Marazzi

et al. 2018

Photochem Photobiol Sci

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Benzophenone (BP) despite its relatively simple molecular structure is a paradigmatic sensitizer, featuring both photocatalytic and photobiological effects due to its rather complex photophysical properties. In this contribution we report an original theoretical approach to model realistic, ultra-fast spectroscopy data, which requires describing intra- and intermolecular energy and structural relaxation. In particular we explicitly simulate time-resolved pump-probe spectra using a combination of state-of-the art hybrid quantum mechanics/molecular mechanics dynamics to treat relaxation and vibrational effects. The comparison with experimental transient absorption data demonstrates the efficiency and accuracy of our approach. Furthermore the explicit inclusion of the solvent, water for simulation and methanol for experiment, allows us, despite the inherent different behavior of the two, to underline the role played by the H-bonding relaxation in the first hundreds of femtoseconds after optical excitation. Finally we predict for the first time the two-dimensional electronic spectrum (2DES) of BP taking into account the vibrational effects and hence modelling partially symmetric and asymmetric ultrafast broadening.

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Probing the Photodynamics of Rhodopsins with Reduced Retinal Chromophores

Cited by 53 publications

References 41 publications

The Fractional Occupation Number Weighted Density as a Versatile Analysis Tool for Molecules with a Complicated Electronic Structure

The Fractional Occupation Number Weighted Density as a Versatile Analysis Tool for Molecules with a Complicated Electronic Structure

Photoisomerization of Arylazopyrazole Photoswitches: Stereospecific Excited‐State Relaxation

The effect of solvent relaxation in the ultrafast time-resolved spectroscopy of solvated benzophenone

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