Double refined bonding model

Most of the kinetic models predict that the sulfite ion radical is easily oxidized by 02 and/or the oxidized form of the catalyst, but this species was rarely considered as a potential oxidant. In a recent pulse radiolysis study, the oxidation of Ni(II and I) and Cu(II and I) macrocyclic complexes by SO was studied under anaerobic conditions (117). In the reactions with Ni(I) and Cu(I) complexes intermediates could not be detected, and the electron transfer was interpreted in terms of a simple outer-sphere mechanism. In contrast, time resolved spectra confirmed the formation of intermediates with a ligand-radical nature in the reactions of the M(II) ions. The formation of a product with a sulfonated macrocycle and another with an additional double bond in the macrocycle were isolated in the reaction with [NiCR]2+. These results may require the refinement of the kinetic model proposed by Lepentsiotis for the [NiCR]2+ SO/ 02 system (116). 

Formal replacement of one double bond in thiepin (51) by a sulfur atom leads to 1,2- (53) and 1,4-dithiin (54). The latter compound has been synthesized,70 and it is a non-planar, thermally stable molecule with a reactivity widely different from that of aromatic systems. A refined HMO method (Model B)71 has been used successfully to explain known properties of 54, and remarkably good agreement was obtained between the calculated and experimental C—S—C and C—C—S bond angles. For the parameters used (8S =0, pcc = 1.06, pcs = 0.77), the highest occupied orbital is anti-bonding, in agreement with the high... 

Structural refinements of the low temperature phase quickly showed that the Pa3 model was correct.[Da91] Furthermore, they gave an explanation for the curious pattern of fullerene orientations within the lattice. The chosen orientation optimizes the electrostatic interaction between fullerenes, by placing electron-poor pentagons in opposition to electron rich double bonds. 

Based on the above considerations, the refined model of the thin filament is presented in Fig. 9B (Ohtsuki, 1974 Ebashi, 1980). In this second model, the position of end-to-end bonding of tropomyosins is indicated, and the two troponin-tropomyosin filaments in the grooves of actin double strands are shifted by half the actin size relative to each other. The shift between two troponin-tropomyosin filaments has been verified by X-ray diffraction studies on invertebrate striated muscles (Wray et al., 1978 Maeda et al., 1979 Namba et al., 1980). The fact that the distance between the top of the thin filament and the position of the nearest troponin is 27 nm (i.e., two-thirds of the troponin period length) (Ohtsuki, 1974) indicates that the top of the filament is situated at the left in the model of the thin filament of Fig. 9B. 

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). 

However, the stereochemical consequence of one-photon-two-bond isomerization for this model is not in agreement with experimental fact. Subsequently, the model was modified to one that involved small twists at various double and single bonds (none greater than 90°), thus leading to one-bond isomerization only. The revised model appears to us a refined OBF process (i.e., a modified version of the conventional torsional relaxation) rather than a modified BP, as claimed. 

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