Bicyclic pedal

Warshel, A. (1976) Bicycle-Pedal Model for the First Step in the Vision Process, Nature 260, 679-683. 

Several years ago, we found that the isomerization of n-butylammonium ( Z,Z)-muconate produces the corresponding EE-isomer in a high yield in the crystalline state under photoirradiation [41]. This solid-state photoisomerization was re e e< t0 he a one-way reaction and no EZ-isomer was formed during the reaction, unsaturated compounds such as olefins, polyenes, and azo compounds generally undergo reversible one-bonded photoisomerization to form a mixture of omers. Previously, we pointed out the possibility that the isomerization of the but thni(i er Va ves the s°hd state f°ll°ws the bicycle-pedal reaction mechanism, et al [4 eta s °ffhe molecular dynamics ofthe reaction had not been clarified. Saltiel react an< fl have independently discussed volume-conserving... 

V a one-bond-flip (OBF), bicycle-pedal (BP), > Models. The OBT and HT models include... 

Thus, we clarified the isomerization process of the muconates according to a bicycle-pedal model. The isomerization occurs via a topochemical reaction process which does not require significant movement of the atoms. The void space included in the crystals plays an important role in the phase transition rather than in the isomerization. In future, the photochemical process of polyene systems performed in confined media will be further clarified using a simple model such as the isomerization of the muconates. 

I, 4-di-o-tolyl-l,3-butadiene in glassy media at 77 K one-bond-twist and bicycle-pedal mechanisms. Angew. Chem. Int. Ed., 47, 1237-1240. 

Three different photoisomerization mechanisms of singlet excited polyenes have been proposed (1) one-bond twist, a typical process observed in fluid solutions but also in glassy media,525 553 565 (2) the bicycle-pedal mechanism involving simultaneous rotation about two original double bonds, assumed to occur in a constraining environment,566-568 and (3) a volume-conserving two-bond hula twist 531 569 510 (Scheme 6.7). In some cases, the existence of the last mechanism has been ruled... 

Explain the following concepts and keywords photostationary state Rydberg state NEER principle bicycle-pedal mechanism phototransduction phototherapy photochemical deracemization enantiodifferentiating photosensitization photochromism di-Tt-methane rearrangement asymmetric photochemical synthesis single-crystal-to-single-crystal photochemistry photochemotherapy rule of five. 

The hula twist mechanism (HT, Fig. 2.3B), first validated with carotenoids, is not consistent with the time-scale of photoisomerization of chromoproteins since CTI of the retinal chromophore, which is inserted deep inside the protein, necessitates a major reorganization of the peptide molecular framework. Therefore, a new volume-conserving mechanism, called bicyclic pedal (BP, Fig. 2.3C), was proposed. In fact, all these mechanisms are still a topic of discussion since chromoprotein photo-intermediates highlighted by recent studies do not confirm this hypothesis. In particular, several photo-products of the retinal Schiff base in the... 

Due to constraints of space, I could not introduce many important theoretical studies here. Various important models have been proposed on the primary isomerization mechanism in rhodopsins, including the bicycle pedal model [101], sudden polarization [102], and the hula-twist model [103]. The finding of a conical intersection between the excited and ground states is also an important contribution [104]. Since the atomic structures of visual and archaeal rhodopsins are now available, theoretical investigations will become more important in the future. The combination of three methods - diffraction, spectroscopy, and theory - will lead to a real understanding of the isomerization mechanism in rhodopsins. 

Figure 1-24. The Gossamer Albatross, a human-powered all-plastic airplane that conquered the English Channel in 1979, used Du Font s Mylar bioriented TP polyester film, Kevlar aramid fiber, Delrin acetal resin. Dacron TP polyester fiber, and nylon as key elements in its construction. This innovative use of lightweight engineered plastics used bicycle pedals to provide power to a propeller.

Schapiro, I., Weingart, O., Buss, V. (2009). Bicycle-pedal isomerization in a rhodopsin chromophore model. Journal of the American Chemical Society, 131(1), 16. doi 10.1021/ Ja805586z. 

More than 30 years ago Warshel proposed, on the basis of semiempirical simulations, an isomerization mechanism that could explain how this process can occur in the restricted space of the Rh binding pocket (Warshel 1976). Since two adjacent double bonds were found to isomerize simultaneously the mechanism reveal a so-called bicycle pedal motion. Due to the concerted rotation of two double bonds in opposite directions the overall conformational change is minimized and hence this mechanism was found to be space-saving. The empirical valence bond (EVB) method (Warshel and Levitt 1976) was used to compute the excited state potential energy surface of the chromophore during a trajectory calculation where the steric effects of the protein matrix were modeled by specific restraints on the retinal atoms. Since then, Warshel and his coworkers have improved the model employing better structural data and new computational developments (Warshel and Barboy 1982 Warshel and Chu 2001 Warshel et al. 1991). The main refinement of the bicycle pedal mechanism was that the simultaneous rotation of the adjacent double bonds is aborted at a twist of 40° and leads to the isomerization of only one bond (Warshel and Barboy 1982). 

The X-ray structures of as-synthesized and its daughter products reveal step by step reversible bicycle-pedal or crankshaft motion of the azo group (Scheme 8). Similar dynamic pedal motion was also observed in a Zn(II)-based framework [48]. 

---