Protonated Schiff-base of retinal

Figure 2-3. Protonated Schiff-base of retinal (PSBR) and computational models used in ONIOM QM QM calculations (left). Electrostatic effects of the surrounding protein on excitation energies in bacteriorhodopsin evaluated using TD-B3LYP Amber right). (Adapted from Vreven and Morokuma [37] (Copyright American Institute of Physics) and Vreven et al. [38], Reprinted with permission.)...

Ultrafast photophysics of the protonated Schiff base of retinal in alcohols studied by femtosecond fluorescence up-conversion... 

While 11 -cis-retinal absorbs at 380 nm and a model protonated Schiff base of retinal with n-butylamine in methanol [210,211] absorbs at 440 nm, the absorption maxima of visual pigments based on 11 -cis-retinal span a wide range of values, from 430 to ca. 600 nm. Therefore, the problem consists of determining the nature of the... 

Fig. 15. Rapid-flow resonance Raman spectra of protonated Schiff bases of retinals in ethanol (chloride salts of protonated n-butylamine derivatives). (A) 11 -ds isomer. (B) 9-cis isomer. (C) 13-cis isomer. (D) all-trans isomer 651...

Baasov, T., and Sheves, M., C=C stretching vibrational frequencies in the model compounds of protonated Schiff bases of retinal, Angew. Chem., 96, 786, 1984. 

Yamada, A., T. Kakitani, et al. (2002). A computational study on the stability of the protonated Schiff base of retinal in rhodopsin. Chemical Physics Letters 366(5-6) 670-675. 

Calculations of the Potential Energy Curves for the trans-cis Photo-Isomerization of Protonated Schiff Base of Retinal. 

Garavelli, M., Negri, R, Olivucci, M. (1999b). Initial excited-state relaxation of the isolated 11-cis protonated Schiff base of retinal Evidence for in-plane motion from ab initio quantum chemical simulation of the resonance Raman spectrum. Journal of the American Chemical Society, 121(5), 1023-1029. 

Using two-dimensional NMR spectroscopy, the spatial location of various carboxylate anions relative to the polyene chain of the protonated Schiff base of all-fraws-retinal was determined. The observed intermolecular NOE cross-peaks between a proton on the counterion and a proton near the nitrogen atom indicate the existence of ion-pair formation between the protonated retinal Schiff base and various counterions in chloroform. The results suggest that the most likely site of the carboxylate group of the counterion is in the immediate vicinity of the positively charged nitrogen atom of the retinal Schiff base. 

FIGURE 10. Contour plot of two-dimensional nuclear Overhauser effect ll NMR (NOESY) of the protonated Schiff base of all-traos-retinal, in chloroform, with formate as the counterion. The intermolecular NOE cross-peak observed between H15 of the retinal and the counterion proton, at a mixing time of 0.4 s, is shown. Top trace f2 projection of the 2D NOE spectrum. Reproduced by permission of John Wiley Sons from Reference 36... 

P. Du and E. R. Davidson, /. Phys. Chem., 94, 7013 (1990). Ab-Initio Study on the Excitation-Energies of the Protonated Schiff-Base of 11-c/s-Retinal. 

Akhtar et al. [74] proposed that, in rhodopsin, an acceptor group on the protein forms a charge-transfer complex with the unprotonated Schiff base of retinal furthermore, upon ll-cis to trans isomerization, separation of donor and acceptor moieties would occur and the Schiff base linkage would be exposed to hydrolysis. This model can now be discarded as unrealistic the resonance Raman experiments have shown that it is not an unprotonated Schiff base, but a protonated base which is bound to opsin. Further, this and related models were examined by Komatsu and Suzuki [223] using theoretical calculations, who found that charge-transfer type models cannot satisfactorily explain the red shifts seen in visual pigments. 

Schiff Bases. The suggestion that a protonated Schiff base is the primary form of the retinal-opsin binding in natural pigments has stimulated considerable work on the spectroscopic properties of free Schiff bases of retinal (RSB) in solution, especially in their protonated forms (PRSB). Schiff base formation does not alter substantially the spectrum of retinal isomers, being associated with a 20-nm blue shift in the position of the main band, I. Except for the absence of the low-energy (n, tr ) transition, theory predicts only small changes in the location of all other states (75,121). This 1 s been confirmed by the extensive experimental study of Schaffer et al. (75). It appears from theoretical calculations (121) that Schiff bases lack Ag-lfiJ... 

A complex multi-chromophoric system comprises the purple membrane patches from Halobacterium salinarium. These patches are composed of about 3000 bacter-iorhodopsin proteins. The hyperpolarizability of solubilized monomeric bacterio-rhodopsin was measured by HRS and found to be 2100 x 10 esu at 1064 nm. This high value is due to the presence of a chromophore in the protein, the proto-nated Schiff base of retinal. A purple membrane patch can be treated as a two-dimensional crystal of bacteriorhodopsin proteins, and its structure is known in considerable detail. The analysis of the purple membrane tensor was performed by adding the hyperpolarizabilities of the individual proteins in the purple membrane. From (depolarized) HRS measurements on purple membrane suspensions, the structure of the purple membrane patches, and an average membrane size measured by atomic force microscopy, a fi value of 2200 x 10 esu was calculated for bacteriorhodopsin [22]. The organization of the dipolar protonated Schiff base chro-mophores in the membranes was found to be predominantly octopolar. 

Fig. 2. A tentative scheme of the bacteriorhodopsin pump. bR indicates the bacteriorhodopsin ground state, and L, M, N(P) and O indicate the corresponding intermediates of the photocycle. NHs, =N2 and =NH represent the protonated Schiff base of the idUtrans retinal residue, the deprotonated and the protonated Schiff bases of 13-cw retinal residues, respectively. -COOH and -COO are the protonated and the deprotonated Asp-96 carboxylic group, respectively. The outward hydrophilic H -conducting pathway (the proton well) is shaded. (From Skulachev[35].)...

Fig. 14. a Protonated Schiff bases of ail-trans and 11-cis retinal, b Sequence of intermediates in the photolysis of rhodopsin. The absorption maximum of each intermediate is shown in parenthesis 651... 

The protonated Schiff base of all-fraws-retinal in the ground state has a pKa greater than 13 [270], which provides its strong connection with the retinal by... 

Fig. 4.1 (A) Structure of human eye. (B) The chromophore of visual rhodopsins, protonated Schiff base of 11-cr s-retinal. This figure is modified from Kandori [5].

Previous HPLC analysis revealed that the protonated Schiff base of 11-cis-retinal in solution is isomerized into the all-trans form almost predominantly, indicating that the reaction pathway in visual rhodopsins is the nature of the chromophore itself [23]. On the other hand, the quantum yield was found to be 0.15 in methanol solution [23]. Therefore, the isomerization reaction is 4—5 times more efficient... 

HPLC analysis also revealed that the protonated Schiff base of all-traws-retinal in solution is isomerized predominantly into the 11-cis form (82% 11-cis, 12% 9-cis, and 6% 13-ds in methanol) [23]. The 11-cis form as a photoproduct is the nature of retinochrome, not those of archaeal rhodopsins. This suggests that the protein environment of retinochrome serves as the intrinsic property of the photoisomerization of the retinal chromophore. In contrast, it seems that the protein environment of archaeal rhodopsins forces the reaction pathway of the isomerization to change into the 13-cis form. In this regard, it is interesting that the quantum yield of bacteriorhodopsin (0.64) is 4—5 times higher than that in solution (-0.15) [21,23], The altered excited state reaction pathways in archaeal rhodopsins never reduce the efficiency. Rather, archaeal rhodopsins discover the reaction pathway from the all-trans to 13-cis form efficiently. Consequently, the system of efficient isomerization reaction is achieved as well as in visual rhodopsins. Structural and spectroscopic studies on archaeal rhodopsins are also reviewed in Section 4.3. 

Figure 4.6B shows typical fluorescence decays of the rhodopsin chromophore, protonated Schiff base of 11-cis-retinal, in methanol solution at 605 and 695 nm. The kinetic features are very similar to those of rhodopsin in terms of ultrafast and nonexponential components (Fig. 4.6A), but the kinetics are considerably slower. The fluorescence lifetimes for five wavelengths obtained in the study [53] were classified by two features the fast femtosecond (90-600 fs) and the slow picosecond (2-3 ps) components. The populations of fast and slow components were 25 and 75%, respectively. Figure 4.6C shows typical fluorescence decays of protonated Schiff base of 11-cis-locked 5-membered retinal in methanol solution... 

Fig. 4.6 The fluorescence decay kinetics of bovine rhodopsin (A), protonated Schiff base of 11-c/s-retinal (PSB11) in methanol (B), and protonated Schiff base of5-membered locked 11 -c/s retinal (5m-PSBll) in methanol (C). The data in (A) are from Kandori et al. [52], while those in (B) and (C) are from Kandori...

---