Stairway to the conical intersection: a computational study of the retinal isomerization

The potential-energy surface of the first excited state of the 11-cis-retinal protonated Schiff base (PSB11) chromophore has been studied at the density functional theory (DFT) level using the time-dependent perturbation theory approach (TDDFT) in combination with Becke's three-parameter hybrid functional (B3LYP). The potential-energy curves for torsion motions around single and double bonds of the first excited state have also been studied at the coupled-cluster approximate singles and doubles (CC2) level. The corresponding potential-energy curves for the ground state have been calculated at the B3LYP DFT and second-order M?ller-Plesset (MP2) levels. The TDDFT study suggests that the electronic excitation initiates a turn of the beta-ionone ring around the C6-C7 bond. The torsion is propagating along the retinyl chain toward the cis to trans isomerization center at the C11=C12 double bond. The torsion twist of the C10-C11 single bond leads to a significant reduction in the deexcitation energy indicating that a conical intersection is being reached by an almost barrierless rotation around the C10-C11 single bond. The energy released when passing the conical intersection can assist the subsequent cis to trans isomerization of the C11=C12 double bond. The CC2 calculations also show that the torsion barrier for the twist of the retinyl C10-C11 single bond adjacent to the isomerization center almost vanishes for the excited state. Because of the reduced torsion barriers of the single bonds, the retinyl chain can easily deform in the excited state. Thus, the CC2 and TDDFT calculations suggest similar reaction pathways on the potential-energy surface of the excited state leading toward the conical intersection and resulting in a cis to trans isomerization of the retinal chromophore. According to the CC2 calculations the cis to trans isomerization mechanism does not involve any significant torsion motion of the beta-ionone ring.     

Quantum dynamics study of fulvene double bond photoisomerization: the role of intramolecular vibrational energy redistribution and excitation energy

The double bond photoisomerization of fulvene has been studied with quantum dynamics calculations using the multi-configuration time-dependent Hartree method. Fulvene is a test case to develop optical control strategies based on the knowledge of the excited state decay mechanism. The decay takes place on a time scale of several hundred femtoseconds, and the potential energy surface is centered around a conical intersection seam between the ground and excited state. The competition between unreactive decay and photoisomerization depends on the region of the seam accessed during the decay. The dynamics are carried out on a four-dimensional model surface, parametrized from complete active space self-consistent field calculations, that captures the main features of the seam (energy and locus of the seam and associated branching space vectors). Wave packet propagations initiated by single laser pulses of 5-25 fs duration and 1.85-4 eV excitation energy show the principal characteristics of the first 150 fs of the photodynamics. Initially, the excitation energy is transferred to a bond stretching mode that leads the wave packet to the seam, inducing the regeneration of the reactant. The photoisomerization starts after the vibrational energy has flowed from the bond stretching to the torsional mode. In our propagations, intramolecular energy redistribution (IVR) is accelerated for higher excess energies along the bond stretch mode. Thus, the competition between unreactive decay and isomerization depends on the rate of IVR between the bond stretch and torsion coordinates, which in turn depends on the excitation energy. These results set the ground for the development of future optical control strategies.     

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.     

H-abstraction is more efficient than cis-trans isomerization in (4-methylcyclohexylidene) fluoromethane. An ab initio molecular dynamics study

Non-adiabatic molecular dynamics simulations have been performed in the fluoro-olefin (4-methylcyclohexylidene) fluoromethane (4MCF) using multiconfigurational CASSCF (complete active space self-consistent field) on-the-fly calculations. As an olefin containing a C[double bond, length as m-dash]C double bond, 4MCF is expected to undergo cis-trans isomerization after light irradiation. However, ab initio molecular dynamics shows that a preferential dissociation of atomic hydrogen is taking place after population transfer to the bright ππ* state. This state is strongly mixed with πσ* states allowing dissociation in the electronic excited state before deactivation to the ground state occurs. A minor amount of trajectories experiences F-dissociation, followed by pyramidalization at the sp(2) carbons and CHF dissociation. In contrast, the amount of trajectories undergoing torsion around the double bond, and therefore cis-trans isomerization, is marginal. The H-abstraction reaction is ultrafast, taking place in less than 60 fs.     

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.     

Steric constraint in the primary photoproduct of an archaeal rhodopsin from regiospecific perturbation of C-D stretching vibration of the retinyl chromophore

In visual and archaeal rhodopsins, light energy is stored in the chromophore-protein interaction after retinal photoisomerization. This paper reports a novel method to monitor the steric constraint after retinal isomerization by use of enhanced C-D stretching vibrations. In the difference FTIR spectra between an archaeal light-sensor pharaonis phoborhodopsin (ppR) and the primary K intermediate at 77 K, no peaks were observed in the 2160-2330 cm-1 region for deuterated retinals at position 7, 8, 10, 11, 12, and 15, whereas a strong peak appeared at 2244 cm-1 for the K intermediate of ppR possessing a C14-D-labeled retinal. The 2244-cm-1 band is assigned as the C14-D stretching vibration, and enhanced absorption in the K state probably originates from the local steric constraint at the C14-D position (also possible electrostatic field effects) after the C13=C14 double bond rotation.     

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.     

The role of the beta-ionone ring in the photochemical reaction of rhodopsin

Time-dependent density functional theory (TDDFT) calculations on the photoabsorption process of the 11-cis retinal protonated Schiff base (PSB) chromophore show that the Franck-Condon relaxation of the first excited state of the chromophore involves a torsional twist motion of the beta-ionone ring relative to the conjugated retinyl chain. For the ground state, the beta-ionone ring and the retinyl chain of the free retinal PSB chromophore form a -40 degrees dihedral angle as compared to -94 degrees for the first excited state. The double bonds of the retinal are shorter for the fully optimized structure of the excited state than for the ground state suggesting a higher cis-trans isomerization barrier for the excited state than for the ground state. According to the present TDDFT calculations, the excitation of the retinal PSB chromophore does not primarily lead to a reaction along the cis-trans torsional coordinate at the C11-C12 bond. The activation of the isomerization center seems to occur at a later stage of the photo reaction. The results obtained at the TDDFT level are supported by second-order M?ller-Plesset (MP2) and approximate singles and doubles-coupled cluster (CC2) calculations on retinal chromophore models; the MP2 and CC2 calculations yield for them qualitatively the same ground state and excited-state structures as obtained in the density functional theory and TDDFT calculations.     

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.     

Vibrational analysis of excited and ground electronic states of all-trans retinal protonated Schiff-bases

We report on vibrational coherence dynamics in excited and ground electronic states of all-trans retinal protonated Schiff-bases (RPSB), investigated by time-resolved Degenerate Four-Wave-Mixing (DFWM). The results show that wave packet dynamics in the excited state of RPSB consist of only low-frequency (<800 cm(-1)) modes. Such low-frequency wave packet motion is observed over a broad range of detection wavelengths ranging from excited state absorption (～500 nm) to stimulated emission (>600 nm). Our results indicate that low-frequency coherences in the excited state are not activated directly by laser excitation but rather by internal vibrational energy redistribution. This is supported by the observation that similar coherence dynamics are not observed in the electronic ground state. Challenging previous experimental results, we show that the formation of low-frequency coherence dynamics in RPSB does not require significant excess vibrational energy deposition in the excited state vibrational manifolds. Concerning ground state wave packet dynamics, we observe a set of high-frequency (>800 cm(-1)) modes, reflecting mainly single and double bond stretching motion in the retinal polyene-chain. Dephasing of these high-frequency coherences is mode-dependent and partially differs from analogous vibrational dephasing of the all-trans retinal chromophore in a protein environment (bacteriorhodopsin).     

The ultrafast photoisomerizations of rhodopsin and bathorhodopsin are modulated by bond length alternation and HOOP driven electronic effects

Rhodopsin (Rh) and bathorhodopsin (bathoRh) quantum-mechanics/molecular-mechanics models based on ab initio multiconfigurational wave functions are employed to look at the light induced π-bond breaking and reconstitution occurring during the Rh → bathoRh and bathoRh → Rh isomerizations. More specifically, semiclassical trajectory computations are used to compare the excited (S(1)) and ground (S(0)) state dynamics characterizing the opposite steps of the Rh/bathoRh photochromic cycle during the first 200 fs following photoexcitation. We show that the information contained in these data provide an unprecedented insight into the sub-picosecond π-bond reconstitution process which is at the basis of the reactivity of the protein embedded 11-cis and all-trans retinal chromophores. More specifically, the data point to the phase and amplitude of the skeletal bond length alternation stretching mode as the key factor switching the chromophore to a bonding state. It is also confirmed/found that the phase and amplitude of the hydrogen-out-of-plane mode controls the stereochemical outcome of the forward and reverse photoisomerizations.     

Harmonic and anharmonic features of IR and NIR absorption and VCD spectra of chiral 4-X-[2.2]paracyclophanes

The vibrational absorption spectra and vibrational circular dichroism (VCD) spectra of both enantiomers of 4-X-[2.2]paracyclophanes (X = COOCD3, Cl, I) have been recorded for a few regions in the range of 900-12000 cm(-1). The analysis of the VCD spectra for the two IR regions, 900-1600 cm(-1) and 2800-3200 cm(-1), is conducted by comparing with DFT calculations of the corresponding spectra; the latter region reveals common motifs of vibrational modes for the three molecules for aliphatic CH stretching fundamentals, whereas in the mid-IR region, one is able to identify specific signatures arising from the substituent groups X. In the CH stretching region between 2900 and 2800 cm(-1), we identify and interpret a group of three IR VCD bands due to HCH bending overtone transitions in Fermi resonance with CH stretching fundamental transitions. The analysis of the NIR region between approximately 8000 and approximately 9000 cm(-1) for X = COOCD3 reveals important features of the aromatic CH stretching overtones that are of value since the aromatic CH stretching fundamentals are almost silent. The intensifying of such overtones is attributed to electrical anharmonicity terms, which are evaluated here by ab initio methods and compared with literature data.     

Molecular Dynamics Simulation of the Excited-State Dynamics of Bacteriorhodopsin

Abstract— The excited-state dynamics of bacteriorhodopsin was studied by molecular dynamics simulation. For the purpose of suppressing large displacement of amino acid residues on the surface of bacteriorhodopsin, positional restraints were imposed on these residues. A new method was developed to investigate the movement of amino acid residues upon photoexcitation and their role on the ultrafast photoisomerization of the chromophore. The structural change of bacteriorhodopsin was then traced up to 200 fs, i.e. until the formation of the intermediate I. We found that when all the conjugated bonds of the chromophore were allowed to twist freely in the excited state, many bonds including the C13=C14 bond twist in large scale within 100 fs. When only the C13=C14 bond and the single bonds were allowed to twist freely, the twisting took place at most 20° within 200 fs. From these results, it is claimed that a special potential surface is provided for the C13=C14 bond twisting by the protein environment in the course of the isomerization reaction, giving rise to the specific, ultrafast photoisomerization of bacteriorhodopsin. As a trace of such a mechanism, we observed that several functionally important residues incuding Asp85, Asp212 and Tyr185 responded quickly to the photoexcitation of the chromophore.     

Determination of the chromophore structures in the photoinduced reaction cycle of phytochrome

The chromophore structures in the parent states Pr and Pfr as well as in the photocycle intermediate Lumi-R of oat phytochrome phyA are determined by comparison of the experimental resonance Raman spectra with calculated Raman spectra that have been obtained by density functional theory calculations (B3LYP) using scaled force fields. The spectra were calculated for various tetrapyrrole geometries including more than twenty different methine bridge isomers. For the parent states Pr and Pfr the best agreement in terms of vibrational frequencies, isotopic shifts, and Raman intensities was achieved with the ZZZasa and ZZEssa geometry, respectively. For the first intermediate Lumi-R, the chromophore geometry is concluded to be the ZZEasa configuration. These finding imply that the primary step of the photoactivation of phytochrome is the Z/E isomerization of the C-D methine bridge double bond, whereas the single bond remains in the anti conformation. The subsequent transition to the physiologically active state Pfr includes a (partial) single bond rotation of the A-B methine bridge.     

Efficient π-electron conjugated push-pull nonlinear optical chromophore 1-(4-methoxyphenyl)-3-(3,4-dimethoxyphenyl)-2-propen-1-one: A vibrational spectral study

As part of the efforts for the design new organic nonlinear optical (NLO) materials with high efficiency for present day technological requirements, a comprehensive investigation on the intramolecular charge transfer (ICT) of an efficient π-conjugated potential push-pull NLO chromophore, 1-(4-methoxyphenyl)-3-(3,4-dimethoxyphenyl)-2-propen-1-one to a strong electron acceptor group through the π-conjugated bridge has been carried out from their vibrational spectra. The NIR FT-Raman and FT-IR spectra supported by the density functional theory (DFT) quantum chemical computations have been employed to analyze the effects of intramolecular charge transfer on the geometries and the vibrational modes contributing to the linear electro-optic effect of the organic NLO material. The calculated first hyperpolarizability of DMMC is 6.650 × 10⁻³⁰ esu, which is 25 times that of urea. The simultaneous IR and Raman activation of the phenyl ring modes of ν(CC/C-C) mode, ring CC stretching modes, in-plane deformation modes and the umbrella mode of methyl groups also provide evidences for the charge transfer interaction between the donors and the acceptor group through the π-system. Vibrational analysis indicates the electronic effects such as induction and back-donation on the methyl hydrogen atoms causing the lowering of stretching wavenumbers have also been analyzed in detail. The planar conformations would give an enhanced NLO activity where as any deviations from planarity would decrease the mobility of electrons within the π-conjugated molecular system, resulting a reduction in NLO activity.     

Vibrational Spectra and Molecular Vibrational Behaviors of All-Carboatomic Rings,cyclo[18]carbon and Its Analogues

The vibrational spectra of cyclo[18]carbon and its analogues, cyclo[2n]carbon (n=3 to 15), were carefully simulated and characterized. The in-plane C−C stretching vibrations shows strong rigidity, while out-of-plane motions seem to be extremely flexible. The solvation effect can enhance signal strengths of the vibrational spectra, but does not evidently change the shape of the spectral curves. The infrared and Raman spectra of cyclo[2n]carbons are quite sensitive to ring size in the range of n=3 to 7, while the size only modestly affects peak positions and strengths for larger rings. Molecular dynamic trajectories show that the fluctuation period of the skeleton of cyclo[18]carbon is basically constant at different temperatures, and they are all about 300 fs. With increase of simulation temperature, the ring distortion due to thermal motion is notable and becomes much stronger. However, neither ring breaking nor isomerization in cyclo[18]carbon is observed during the simulations untill 298.15 K.     

Structural and vibrational studies of molecular conductors using quantum mechanical methods: 1,3-Dithiole-2-thione, 1,3-dithiole-2-one, 1,3-dioxole-2-one and 1,3-dioxole-2-thione

Computations were carried out by employing the RHF and density functional theory (DFT) methods to investigate the geometries, atomic charges, harmonic vibrational frequencies for the 1,3-dithiole-2-thione (DTT), 1,3-dithiole-2-one (DTO), 1,3-dioxole-2-thione (DOT) and 1,3-dioxole-2-one (DOO) molecules and their radical cations. The geometrical parameters and atomic charges on various atomic sites of the DTT and DOT molecules and their radical cations suggest extended conjugation in these systems. Contrary to this, for the DOO⁺ and DTO⁺ ions there is no evidence in favour of such conjugation, however, the neutral molecules exhibit some conjugation. Harmonic forced field and vibrational mode calculations provided convincing theoretical evidence for the reassignment of some fundamental vibrational modes for all the four molecules. In going from the neutral species to the charged ions for all the four cases the CC stretching frequency is found to decrease drastically. The CS stretching frequency reduces drastically for the DTT and DOT molecules as compared to their radical cations whereas the CO stretching frequency is found to increase in going from the neutral molecule to its radical cation for the DOO and DTO molecules. The ring stretching mode with a₁ symmetry and CC and CO/S stretching modes in these molecules appear to help in conversion of neutral molecule into respective radical cation and neighbouring radical cation into respective neutral molecule. Thus, there appears the feasibility of stretching vibrational mode coupling with electron transfer.     

Coherent low-frequency motions of hydrogen bonded acetic acid dimers in the liquid phase

Ultrafast vibrational dynamics of cyclic hydrogen bonded dimers and the underlying microscopic interactions are studied in temporally and spectrally resolved pump-probe experiments with 100 fs time resolution. Femtosecond excitation of the O-H and/or O-D stretching mode gives rise to pronounced changes of the O-H/O-D stretching absorption displaying both rate-like kinetic and oscillatory components. A lifetime of 200 fs is measured for the v=1 state of the O-H stretching oscillator. The strong oscillatory absorption changes are due to impulsively driven coherent wave packet motions along several low-frequency modes of the dimer between 50 and 170 cm(-1). Such wave packets generated via coherent excitation of the high-frequency O-H/O-D stretching oscillators represent a clear manifestation of the anharmonic coupling of low- and high-frequency modes. The underdamped low-frequency motions dephase on a time scale of 1-2 ps. Calculations of the vibrational potential energy surface based on density functional theory give the frequencies, anharmonic couplings, and microscopic elongations of the low-frequency modes, among them intermolecular hydrogen bond vibrations. Oscillations due to the excitonic coupling between the two O-H or O-D stretching oscillators are absent as is independently confirmed by experiments on mixed dimers with uncoupled O-H and O-D stretching oscillators.     

Time-resolved resonance Raman analysis of chromophore structural changes in the formation and decay of rhodopsin's BSI intermediate

Time-resolved resonance Raman microchip flow experiments are performed to obtain the vibrational spectrum of the chromophore in rhodopsin's BSI intermediate and to probe structural changes in the bathorhodopsin-to-BSI and BSI-to-lumirhodopsin transitions. Kinetic Raman spectra from 250 ns to 3 micros identify the key vibrational features of BSI. BSI exhibits relatively intense HOOP modes at 886 and 945 cm(-1) that are assigned to C(14)H and C(11)H=C(12)H A(u) wags, respectively. This result suggests that in the bathorhodopsin-to-BSI transition the highly strained all-trans chromophore has relaxed in the C(10)-C(11)=C(12)-C(13) region, but is still distorted near C(14). The low frequency of the 11,12 A(u) HOOP mode in BSI compared with that of lumirhodopsin and metarhodopsin I indicates weaker coupling between the 11H and 12H wags due to residual distortion of the BSI chromophore near C(11)=C(12). The C=NH(+) stretching mode in BSI at 1653 cm(-1) exhibits a normal deuteriation induced downshift of 23 cm(-1), implying that there is no significant structural rearrangement of the Schiff base counterion region in the transition of bathorhodopsin to BSI. However, a dramatic Schiff base environment change occurs in the BSI-to-lumirhodopsin transition, because the 1638 cm(-1) C=NH(+) stretching mode in lumirhodopsin is unusually low and shifts only 7 cm(-1) in D(2)O, suggesting that it has essentially no H-bonding acceptor. With these data we can for the first time compare and discuss the room temperature resonance Raman vibrational structure of all the key intermediates in visual excitation.