Ultrafast excited-state dynamics of tetraphenylethylene studied by semiclassical simulation

Detailed simulation study is reported for the excited-state dynamics of photoisomerization of cis-tetraphenylethylene (TPE) following excitation by a femtosecond laser pulse. The technique for this investigation is semiclassical dynamics simulation, which is described briefly in the paper. Upon photoexcitation by a femtosecond laser pulse, the stretching motion of the ethylenic bond of TPE is initially excited, leading to a significant lengthening of ethylenic bond in 300 fs. Twisting motion about the ethylenic bond is activated by the energy released from the relaxation of the stretching mode. The 90 degrees twisting about the ethylenic bond from an approximately planar geometry to nearly a perpendicular conformation in the electronically excited state is completed in 600 fs. The torsional dynamics of phenyl rings which is temporally lagging behind occurs at about 5 ps. Finally, the twisted TPE reverts to the initial conformation along the twisting coordinate through nonadiabatic transitions. The simulation results provide a basis for understanding several spectroscopic observations at molecular levels, including ultrafast dynamic Stokes shift, multicomponent fluorescence, viscosity dependence of the fluorescence lifetime, and radiationless decay from electronically excited state to the ground state along the isomerization coordinate.     

Constraints of opsin structure on the ligand-binding site: studies with ring-fused retinals

Ring-fused retinal analogs were designed to examine the hula-twist mode of the photoisomerization of the 9-cis retinylidene chromophore. Two 9-cis retinal analogs, the C11-C13 five-membered ring-fused and the C12-C14 five-membered ring-fused retinal derivatives, formed the pigments with opsin. The C11-C13 ring-fused analog was isomerized to a relaxed all-trans chromophore (lambda(max) > 400 nm) at even -269 degrees C and the Schiff base was kept protonated at 0 degrees C. The C12-C14 ring-fused analog was converted photochemically to a bathorhodopsin-like chromophore (lambda(max) = 583 nm) at -196 degrees C, which was further converted to the deprotonated Schiff base at 0 degrees C. The model-building study suggested that the analogs do not form pigments in the retinal-binding site of rhodopsin but form pigments with opsin structures, which have larger binding space generated by the movement of transmembrane helices. The molecular dynamics simulation of the isomerization of the analog chromophores provided a twisted C11-C12 double bond for the C12-C14 ring-fused analog and all relaxed double bonds with a highly twisted C10-C11 bond for the C11-C13 ring-fused analog. The structural model of the C11-C13 ring-fused analog chromophore showed a characteristic flip of the cyclohexenyl moiety toward transmembrane segments 3 and 4. The structural models suggested that hula twist is a primary process for the photoisomerization of the analog chromophores.     

Sub-5-fs real-time spectroscopy of transition states in bacteriorhodopsin during retinal isomerization

By using a sub-5-fs visible laser pulse, we have made the first observation of the vibrational spectra of the transition state during trans-cis isomerization in the retinal chromophore of bacteriorhodopsin (bR(S68). No instant isomerization of the retinal occurs in spite of electron promotion from the bonding pi-orbital to the anti-bonding pi*-orbital. The difference between the in-plane and out-of-plane vibrational frequencies (about 1150-1250 and 900-1000 cm(-1), respectively) is reduced during the first time period. The vibrational spectra after this period became very broad and weak and are ascribed to a "silent state." The silent state lasts for 700-900 fs until the chromophore isomerizes to the cis-C13 = C14 conformation. The frequency of the C = C stretching mode was modulated by the torsion mode of the C13 = C14 double bond with a period of 200 fs. The modulation was clearly observed for four to five periods. Using the empirical equation for the relation between bond length and stretching frequency, we determined the transitional C = C bond length with about 0.01 angstroms accuracy during the torsion motion around the double bond with 1-fs time resolution.     

Early time hydrogen-bonding dynamics of photoexcited coumarin 102 in hydrogen-donating solvents: theoretical study

To study the early time hydrogen-bonding dynamics of chromophore in hydrogen-donating solvents upon photoexcitation, the infrared spectra of the hydrogen-bonded solute-solvent complexes in electronically excited states have been calculated using the time-dependent density functional theory (TDDFT) method. The hydrogen-bonding dynamics in electronically excited states can be widely monitored by the spectral shifts of some characteristic vibrational modes involved in the formation of hydrogen bonds. In this study, we have demonstrated that the intermolecular hydrogen bonds between coumarin 102 (C102) and hydrogen-donating solvents are strengthened in the early time of photoexcitation to the electronically excited state by theoretically monitoring the stretching modes of C=O and H-O groups. This is significantly contrasted with the ultrafast hydrogen bond cleavage taking place within a 200-fs time scale upon electronic excitation, proposed in many femtosecond time-resolved vibrational spectroscopy experiments. The transient hydrogen bond strengthening behaviors in excited states of chromophores in hydrogen-donating solvents, which we have demonstrated here for the first time, may take place widely in many other systems in solution and are very important to explain the fluorescence-quenching phenomena associated with some radiationless deactivation processes, for example, the ultrafast solute-solvent intermolecular electron transfer and the internal conversion process from the fluorescent state to the ground state.     

Torsion potential works in rhodopsin

We investigate the role of protein environment of rhodopsin and the intramolecular interaction of the chromophore in the cis-trans photoisomerization of rhodopsin by means of a newly developed theoretical method. We theoretically produce modified rhodopsins in which a force field of arbitrarily chosen part of the chromophore or the binding pocket of rhodopsin is altered. We compare the equilibrium conformation of the chromophore and the energy stored in the chromophore of modified rhodopsins with those of native rhodopsins. This method is called site-specific force field switch (SFS). We show that this method is most successfully applied to the torsion potential of rhodopsin. Namely, by reducing the twisting force constant of the C11=C12 of 11-cis retinal chromophore of rhodopsin to zero, we found that the equilibrium value of the twisting angle of the C11=C12 bond is twisted in the negative direction down to about -80 degrees. The relaxation energy obtained by this change amounts to an order of 10 kcal/mol. In the case that the twisting force constant of the other double bond is reduced to zero, no such large twisting of the bond happens. From these results we conclude that a certain torsion potential is applied specifically to the C11=C12 bond of the chromophore in the ground state of rhodopsin. This torsion potential facilitates the bond-specific cis-trans photoisomerization of rhodopsin. This kind of the mechanism is consistent with our torsion model proposed by us more than a quarter of century ago. The origin of the torsion potential is analyzed in detail on the basis of the chromophore structure and protein conformation, by applying the SFS method extensively.     

Electronic optical activity of (−)-α-phellandrene

Molecular orbital computations on the sign and magnitude of the Cotton effect of (?)-α-phellandrene (a conjugated diene) and the separate twisted butadiene chromophore were performed using configuration interaction (CI) and the random phase approximation (RPA) methods with a standard minimal basis set of STO/3G orbitals. The relative contributions to the rotatory strength of (?)-α-phellandrene which arise from a twist in the diene unit, the allylic axial bond, and nonplanarity of either one or both of the C?C double bonds were determined by examining various molecular geometries. This theoretical study confirms that the allylic axial substituent/bond provides the largest contribution to the longwavelength Cotton effect. It is found that the rotatory strength arising from distortion of the planar geometry of the double bonds tends to cancel the rotatory strength arising from the sense of twist of the diene unit. The computed energies suggest that molecular geometries where the trisubstituted bond is kept planar, and where twisting is allowed about the cis double bond, may be favored over geometries where torsion is allowed about both double bonds.     

The Photocycle of Channelrhodopsin‐2: Ultrafast Reaction Dynamics and Subsequent Reaction Steps

The photocycle of channelrhodopsin‐2 is investigated in a comprehensive study by ultrafast absorption and fluorescence spectroscopy as well as flash photolysis in the visible spectral range. The ultrafast techniques reveal an excited‐state decay mechanism analogous to that of the archaeal bacteriorhodopsin and sensory rhodopsin II from Natronomonas pharaonis. After a fast vibrational relaxation of the excited‐state population with 150 fs its decay with mainly 400 fs is observed. Hereby, both the initial all‐trans retinal ground state and the 13‐cis‐retinal K photoproduct are populated. The reaction proceeds with a 2.7 ps component assigned to cooling processes. Small spectral shifts are observed on a 200 ps timescale. They are attributed to conformational rearrangements in the retinal binding pocket. The subsequent dynamics progresses with the formation of an M‐like intermediate (7 and 120 μs), which decays into red‐shifted states within 3 ms. Ground‐state recovery including channel closing and reisomerization of the retinal chromophore occurs in a triexponential manner (6 ms, 33 ms, 3.4 s). To learn more about the energy barriers between the different photocycle intermediates, temperature‐dependent flash photolysis measurements are performed between 10 and 30 °C. The first five time constants decrease with increasing temperature. The calculated thermodynamic parameters indicate that the closing mechanism is controlled by large negative entropy changes. The last time constant is temperature independent, which demonstrates that the photocycle is most likely completed by a series of individual steps recovering the initial structure.     

Subpicosecond protein backbone changes detected during the green-absorbing proteorhodopsin primary photoreaction

Recent studies demonstrate that photoactive proteins can react within several picoseconds to photon absorption by their chromophores. Faster subpicosecond protein responses have been suggested to occur in rhodopsin-like proteins where retinal photoisomerization may impulsively drive structural changes in nearby protein groups. Here, we test this possibility by investigating the earliest protein structural changes occurring in proteorhodopsin (PR) using ultrafast transient infrared (TIR) spectroscopy with approximately 200 fs time resolution combined with nonperturbing isotope labeling. PR is a recently discovered microbial rhodopsin similar to bacteriorhodopsin (BR) found in marine proteobacteria and functions as a proton pump. Vibrational bands in the retinal fingerprint (1175-1215 cm(-1)) and ethylenic stretching (1500-1570 cm(-1)) regions characteristic of all-trans to 13-cis chromophore isomerization and formation of a red-shifted photointermediate appear with a 500-700 fs time constant after photoexcitation. Bands characteristic of partial return to the ground state evolve with a 2.0-3.5 ps time constant. In addition, a negative band appears at 1548 cm(-1) with a time constant of 500-700 fs, which on the basis of total-15N and retinal C15D (retinal with a deuterium on carbon 15) isotope labeling is assigned to an amide II peptide backbone mode that shifts to near 1538 cm(-1) concomitantly with chromophore isomerization. Our results demonstrate that one or more peptide backbone groups in PR respond with a time constant of 500-700 fs, almost coincident with the light-driven retinylidene chromophore isomerization. The protein changes we observe on a subpicosecond time scale may be involved in storage of the absorbed photon energy subsequently utilized for proton transport.     

STUDIES ON CHROMOPHORE COUPLING IN ISOLATED PHYCOBILIPROTEINS. IV. FEMTOSECOND TRANSIENT ABSORPTION STUDY OF ULTRAFAST EXCITED STATE DYNAMICS IN TRIMERIC PHYCOERYTHROCYANIN COMPLEXES*

The excited state dynamics of trimeric phycoerythrocyanin has been studied by two-color femtosecond transient absorption spectroscopy with a time-resolution better than 200 fs. Upon selective excitation of the short-wavelength phycobiliviolin chromophore at 575 nm absorption bleachings are observed. An isotropic ultrafast decay of the initial bleaching of 585 ± 40 fs has been resolved at short detection wavelength (578 nm). Upon stepwise increase of the detection wavelength up to 617 nm, the bleaching showed a delayed rise above 593 nm with r_rice=380–580 fs. All other isotropic kinetic components in this wavelength range were longer than 100 ps. The ultrafast component is discussed in terms of an energy transfer process from the α-84 phycobiliviolin chromophore to the β-84 chromophore in adjacent monomer subunits of the trimer. It is concluded that the β-155 chromophore is the longest-wavelength chromophore. Exciton relaxation between closely spaced chromophore pairs is discussed as an alternative interpretation for the ultrafast component.     

On the Role of Hydrogen Bonds in Photoinduced Electron‐Transfer Dynamics between 9‐Fluorenone and Amine Solvents

Using ultrafast fluorescence upconversion and mid‐infrared spectroscopy, we explore the role of hydrogen bonds in the photoinduced electron transfer (ET) between 9‐fluorenone (FLU) and the solvents trimethylamine (TEA) and dimethylamine (DEA). FLU shows hydrogen‐bond dynamics in the methanol solvent upon photoexcitation, and similar effects may be anticipated when using DEA, whereas no hydrogen bonds can occur in TEA. Photoexcitation of the electron‐acceptor dye molecule FLU with a 400 nm pump pulse induces ultrafast ET from the amine solvents, which is followed by 100 fs IR probe pulses as well as fluorescence upconversion, monitoring the time evolution of marker bands of the FLU S₁ state and the FLU radical anion, and an overtone band of the amine solvent, marking the transient generation of the amine radical cation. A comparison of the experimentally determined forward charge‐separation and backward charge‐recombination rates for the FLU‐TEA and FLU‐DEA reaction systems with the driving‐force dependencies calculated for the forward and backward ET rates reveals that additional degrees of freedom determine the ET reaction dynamics for the FLU‐DEA system. We suggest that hydrogen bonding between the DEA molecules plays a key role in this behaviour.     

Photoisomerization in proteorhodopsin mutant D97N

The first steps of the photocycle of the D97N mutant of proteorhodopsin (PR) have been investigated by means of ultrafast transient absorption spectroscopy. A comparison with the primary dynamics of native PR and D85N mutant of bacteriorhodopsin is given. Upon photoexcitation of the covalently bound all-trans retinal the excited state decays biexponentially with time constants of 1.4 and 20 ps via a conical intersection, resulting in a 13-cis isomerized retinal. Neither of the two-deactivation channels is significantly preferred. The dynamics is slowed down in comparison with native PR at pH 9 and reaction rates are even lower than for native PR at pH 6, where the primary proton acceptor (Asp97) is protonated. Therefore, the ultrafast isomerization is not only controlled by the charge distribution within the retinal binding pocket. This study shows that in addition to direct electrostatics other effects have to be taken into account to explain the catalytic function of Asp97 in PR on the ultrafast isomerization reaction. This may include sterical interactions and/or bound water molecules within the retinal binding pocket.     

Site-selective photoinduced electron transfer from alcoholic solvents to the chromophore facilitated by hydrogen bonding: a new fluorescence quenching mechanism

Solute-solvent intermolecular photoinduced electron transfer (ET) reaction was proposed to account for the drastic fluorescence quenching behaviors of oxazine 750 (OX750) chromophore in protic alcoholic solvents. According to our theoretical calculations for the hydrogen-bonded OX750-(alcohol)(n) complexes using the time-dependent density functional theory (TDDFT) method, we demonstrated that the ET reaction takes place from the alcoholic solvents to the chromophore and the intermolecular ET passing through the site-specific intermolecular hydrogen bonds exhibits an unambiguous site selectivity. In our motivated experiments of femtosecond time-resolved stimulated emission pumping fluorescence depletion spectroscopy (FS TR SEP FD), it could be noted that the ultrafast ET reaction takes place as fast as 200 fs. This ultrafast intermolecular photoinduced ET is much faster than the diffusive solvation process, and even significantly faster than the intramolecular vibrational redistribution (IVR) process of the OX750 chromophore. Therefore, the ultrafast intermolecular ET should be coupled with the hydrogen-bonding dynamics occurring in the sub-picosecond time domain. We theoretically demonstrated for the first time that the selected hydrogen bonds are transiently strengthened in the excited states for facilitating the ultrafast solute-solvent intermolecular ET reaction.     

Theoretical Computer‐Aided Mutagenic Study on the Triple Green Fluorescent Protein Mutant S65T/H148D/Y145F

Green fluorescent protein (GFP) mutant S65T/H148D has been proposed to host a photocycle that involves an excited‐state proton transfer between the chromophore (Cro) and the Asp148 residue and takes place in less than 50 fs without a measurable kinetic isotope effect. It has been suggested that the interaction between the unsuspected Tyr145 residue and the chromophore is needed for the ultrafast sub‐50 fs rise in fluorescence. To verify this, we have performed a computer‐aided mutagenic study to introduce the additional mutation Y145F, which eliminates this interaction. By means of QM/MM molecular dynamics simulations and time‐dependent density functional theory studies, we have assessed the importance of the Cro–Tyr145 interaction and the solvation of Asp148 and shown that in the triple mutant S65T/H148D/Y145F a significant loss in the ultrafast rise of the Stokes‐shifted fluorescence should be expected.     

Tuning of retinal twisting in bacteriorhodopsin controls the directionality of the early photocycle steps

Productive proton pumping by bacteriorhodopsin requires that, after the all-trans to 13-cis photoisomerization of the retinal chromophore, the photocycle proceeds with proton transfer and not with thermal back-isomerization. The question of how the protein controls these events in the active site is addressed here using quantum mechanical/molecular mechanical reaction-path calculations. The results indicate that, while retinal twisting significantly contributes to lowering the barrier for the thermal cis-trans back-isomerization, the rate-limiting barrier for this isomerization is still 5-6 kcal/mol larger than that for the first proton-transfer step. In this way, the retinal twisting is finely tuned so as to store energy to drive the subsequent photocycle while preventing wasteful back-isomerization.     

IDENTIFICATION OF THE PROTON ACCEPTOR OF SCHIFF BASE DEPROTONATION IN BACTERIORHODOPSIN: A FOURIER-TRANSFORM-INFRARED STUDY OF THE MUTANT ASP85 → GLU IN ITS NATURAL LIPID ENVIRONMENT

Abstract— In order to assign the proton acceptor for Schiff base deprotonation in bacteriorhodopsin to a specific Asp residue, the photoreaction of the Asp85 → Glu mutant, as expressed in Halobacterium sp . GRB, was investigated by static low-temperature and time-resolved infrared difference spec-troscopy. Measurements were also performed on the mutant protein labeled with [4-¹³C]Asp which allowed discrimination between Asp and Glu residues. 14,15-di¹³C-retinal was incorporated to distinguish amide-II absorbance changes from changes of the ethylenic mode of the chromophore. In agreement with earlier UV-VIS measurements, our data show that from both the 540 and 610 nm species present in a pH-dependent equilibrium, intermediates similar to K and L can be formed. The 14 ms time-resolved spectrum of the 540 nm species shows that a glutamic acid becomes protonated in the M-like intermediate, whereas the comparable difference spectrum of the 610 nm species demonstrates that in the initial state a glutamic acid is already protonated. In conjunction with earlier observations of protonation of an Asp residue in wild-type M, the data provide direct evidence that the proton acceptor in the deprotonation reaction of the Schiff base is Asp85.     

Environment-dependent ultrafast photoisomerization dynamics in azo dye

Azoaromatic dyes have been extensively investigated over the past decade due to their potential use in a variety of optical devices that exploit their ultrafast photoisomerization processes. Among the azoaromatic dyes, Disperse Red 19 is a commercially available azobenzene nonlinear optical chromophore with a relatively high ground-state dipole moment. In the present study, we used ultrafast time-resolved spectroscopy to clarify the dynamics of a push-pull substituted azobenzene dye. Solution and film samples exhibited different ultrafast dynamics, indicating that the molecular environment affects the photoisomerization dynamics of the dye.     

Ultrafast hydrogen bond strengthening of the photoexcited fluorenone in alcohols for facilitating the fluorescence quenching

The time-dependent density functional theory (TDDFT) method was performed to investigate the excited-state hydrogen-bonding dynamics of fluorenone (FN) in hydrogen donating methanol (MeOH) solvent. The infrared spectra of the hydrogen-bonded FN-MeOH complex in both the ground state and the electronically excited states are calculated using the TDDFT method, since the ultrafast hydrogen-bonding dynamics can be investigated by monitoring the vibrational absorption spectra of some hydrogen-bonded groups in different electronic states. We demonstrated that the intermolecular hydrogen bond C=O...H-O between fluorenone and methanol molecules is significantly strengthened in the electronically excited-state upon photoexcitation of the hydrogen-bonded FM-MeOH complex. The hydrogen bond strengthening in electronically excited states can be used to explain well all the spectral features of fluorenone chromophore in alcoholic solvents. Furthermore, the radiationless deactivation via internal conversion (IC) can be facilitated by the hydrogen bond strengthening in the excited state. At the same time, quantum yields of the excited-state deactivation via fluorescence are correspondingly decreased. Therefore, the total fluorescence of fluorenone in polar protic solvents can be drastically quenched by hydrogen bonding.     

The effect of hydrogen bonding on the excited-state proton transfer in 2-(2'-hydroxyphenyl)benzothiazole: a TDDFT molecular dynamics study

The dynamics of the excited-state proton transfer (ESPT) in a cluster of 2-(2'-hydroxyphenyl)benzothiazole (HBT) and hydrogen-bonded water molecules was investigated by means of quantum chemical simulations. Two different enol ground-state structures of HBT interacting with the water cluster were chosen as initial structures for the excited-state dynamics: (i) an intramolecular hydrogen-bonded structure of HBT and (ii) a cluster where the intramolecular hydrogen bond in HBT is broken by intermolecular interactions with water molecules. On-the-fly dynamics simulations using time-dependent density functional theory show that after photoexcitation to the S(1) state the ESPT pathway leading to the keto form strongly depends on the initial ground state structure of the HBT-water cluster. In the intramolecular hydrogen-bonded structures direct excited-state proton transfer is observed within 18 fs, which is a factor two faster than proton transfer in HBT computed for the gas phase. Intermolecular bonded HBT complexes show a complex pattern of excited-state proton transfer involving several distinct mechanisms. In the main process the tautomerization proceeds via a triple proton transfer through the water network with an average proton transfer time of approximately 120 fs. Due to the lack of the stabilizing hydrogen bond, intermolecular hydrogen-bonded structures have a significant degree of interring twisting already in the ground state. During the excited state dynamics, the twist tends to quickly increase indicating that internal conversion to the electronic ground state should take place at the sub-picosecond scale.     

Revisiting the electronic excited-state hydrogen bonding dynamics of coumarin chromophore in alcohols: Undoubtedly strengthened not cleaved

In the present work, the electronic excited-state hydrogen bonding dynamics of coumarin chromophore in alcohols is revisited. The time-dependent density functional theory (TDDFT) method has been performed to investigate the intermolecular hydrogen bonding between Coumarin 151 (C151) and methanol (MeOH) solvent in the electronic excited state. Three types of intermolecular hydrogen bonds can be formed in the hydrogen-bonded C151–(MeOH)₃ complex. We have demonstrated again that intermolecular hydrogen bonds between C151 and methanol molecules can be significantly strengthened upon photoexcitation to the electronically excited state of C151 chromophore. Our results are consistent with the intermolecular hydrogen bond strengthening in the electronically excited state of Coumarin 102 in alcoholic solvents, which has been demonstrated for the first time by Zhao et al. At the same time, the electronic excited-state hydrogen bond cleavage mechanism of photoexcited coumarin chromophores in alcohols proposed in some other studies about the hydrogen bonding dynamics is undoubtedly excluded. Hence, we believe that the two contrary dynamic mechanisms for intermolecular hydrogen bonding in electronically excited states of coumarin chromophores in alcohols are clarified here.     

Exploring ultrafast H-atom elimination versus photofragmentation pathways in pyrazole following 200 nm excitation

The role of ultraviolet photoresistance in many biomolecules (e.g., DNA bases and amino acids) has been extensively researched in recent years. This behavior has largely been attributed to the participation of dissociative (1)πσ* states localized along X-H (X ═ N, O) bonds, which facilitate an efficient means for rapid nonradiative relaxation back to the electronic ground state via conical intersections or ultrafast H-atom elimination. One such species known to exhibit this characteristic photochemistry is the UV chromophore imidazole, a subunit in the biomolecules adenine and histidine. However, the (1)πσ* driven photochemistry of its structural isomer pyrazole has received much less attention, both experimentally and theoretically. Here, we probe the ultrafast excited state dynamics occurring in pyrazole following photoexcitation at 200 nm (6.2 eV) using two experimental methodologies. The first uses time-resolved velocity map ion imaging to investigate the ultrafast H-atom elimination dynamics following direct excitation to the lowest energy (1)πσ* state (1(1)A" ← X(1)A'). These results yield a bimodal distribution of eliminated H-atoms, situated at low and high kinetic energies, the latter of which we attribute to (1)πσ* mediated N-H fission. The time constants extracted for the low and high energy features are ~120 and <50 fs, respectively. We also investigate the role of ring deformation relaxation pathways from the first optically bright (1)ππ* state (2(1)A' ← X(1)A'), by performing time-resolved ion yield measurements. These results are modeled using a (1)ππ* → ring deformation → photofragmentation mechanism (a model based on comparison with theoretical calculations on the structural isomer imidazole) and all photofragments possess appearance time constants of <160 fs. A comparison between time-resolved velocity map ion imaging and time-resolved ion yield measurements suggest that (1)πσ* driven N-H fission gives rise to the dominant kinetic photoproducts, re-enforcing the important role (1)πσ* states have in the excited state dynamics of biological chromophores and related aromatic heterocycles.