Pedal motion

Pedal motion, a key process of photoreaction in crystals. Is considered to occur only in crystals that have an orientational disorder or a large void around the molecules. 

Fig. 6 The typical disorder of CX3 peripheral groups about the pseudo threefold axis left) and the t) pical pedal motion disorder about the central double bond in E-stilbene kind of molecules right)...

Harada J, Ogawa K (2001) Invisible but common motion in organic crystals a pedal motion in stilbenes and azobenzenes. J Am Chem Soc 123 10884-10888... 

The movement of the produced radical is estimated as shown in Fig. 6.23. Since the cavity is large in the lateral direction, the long -CH2CN part of the photo-produced radical can use this space so as to rotate around the C -C bond like the pedal motion of a bicycle. Therefore, this reaction can proceed without destruction of the single crystal form. For the other two processes, the intermediate radicals suffer from strong steric repulsion in the cavity. This is the reason why the alkyl turn isomerization proceeds in the crystal of III. It is clear that the different pathways from 4-cb to 1-cb in the crystals of I and III are caused by the different reaction cavities for 4-cb groups in the two crystal structures. 

Although the transformation demonstrated here involves large structural change and seems difficult to take place in a crystal, it can easily occur through the motion of a pair of benzene rings analogous to the pedal motion of a bicycle, which is extensively studied in the thermochromism of azobenzenes containing similar molecular skeletons to those of salicylideneanilines [33]. 

The final problem remains why the crystal of 2a showed the color change faster than that of 2p. In the transformation from the enol to trans-keto form, the central -N=CH- plane becomes upside down in the pedal motion, keeping the two phenyl rings in both sides almost unchanged. This means that the rate of the transformation should be affected by the size of reaction cavity for the central -N=CH- group. 

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). 

Schemes Schematic representation of reversible SC-SC pedal motion and twisting of phenyl rings in compound [47] after guest removal by heating (guest molecules are removed for clarity). (Reprinted with permission from Ref. 65. Copyright (2011) American Chemical Society.)...

Figure 42 Guest-triggered supramolecular isomerism in a pillared-layer structure [49] through reversible pedal-motion-type SCSC transformation. DMA = dimethylacetamide, Hjobc=4,4 -oxybisbenzoic acid...

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]. 

Another interesting example of guest-triggered reversible pedal motion in a pillared-layer structure 49, with unusual isomers of paddle wheel SBUs, " was reported by Park et al (Figure 42). The understanding of such molecular motion offers to explain various dynamic aspects of molecules besides being potentially useful in fabricating molecular devices. 

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