Time averaged conformations

The tetraoxahydrospirophosphorane (57) has been isolated in 66% yield from the reaction of (55) with triethylammonium perfluor-opinacolate (56). Hexafluoroacetone inserts into the P-H bond of (57) to form (58) which may also be obtained from (59) as shown1 1. The 1H and 19F n.m.r. spectra of the phosphoranes reveal rapid pseudorotational processes and a time-averaged conformation of a flattened chair for the six-membered rings. 

A single-crystal X-ray structure for a tetraloop compound shows the molecules (not unexpectedly) in a pinched cone conformation (see Figure 5.10a), although the time-averaged conformation deduced from the1H NMR-spectra is C4v-symmetrical (Figure 5.10b). 

The assumption that the polymer spectra and structure correspond to those of the model compounds rests essentially on the approximate correspondence of peak positions. It is important that the spectra be compared at approximately the same temperature, as there is a marked dependence of the peak positions upon temperature. For the polymer at 150°, the peak positions, in -values with respect to the solvent as + 63.8 , are 104.2, 106.0, 125.6, and 127.8. At 25°, the solvent peak position was found to be +63.2 if>, and the model compound peak positions were 106.3, 108.8, 126.6, and 128.9, deviating substantially from the polymer positions. When the model compound spectra are observed at 150°, there is a marked down-field" shift, which brings the - values into much closer correspondence with those of the polymer 104.1, 106.2, 126.2, and 127.7. There appear to be some small relative changes as well, particularly for the meso compound, for the appearance of its AB-type CFa resonance is distinctly temperature dependent. The most likely explanation for this behavior is that it arises from changes in the relative populations of the internal-rotation energy levels, which correspond to changes in the time-averaged conformational structures of the molecules. 

A more useful experimental approach to predicting conformation in a biological environment is through the use of NMR analysis in water. These data, if properly analyzed, give a time average conformation which can be of considerable value in subsequent biological interpretations. It is necessary, however, actually to have the compound under study, and frequently the analysis of the NMR data is extremely complex. 

To further investigate the role of motion in triplet energy transfer, three carotenoporphyrins, 32,33, and 34, were synthesized [73]. In these molecules, the static coupling along the linkage bonds was nearly constant and relatively weak, but the constraints on intramolecular motion differed considerably. From detailed NMR studies in solution the time average conformations were determined. The para-linked isomer (32) was found to be roughly linear, the meta-linked one (33) approximately L shaped, and the ortho-linked one (34) partially folded. 

Fig. 3 depicts the time-averaged position of phenyl acetates in the cavity of a-cyclodextrin, determined by the above method. In these time-averaged conformations, the centers of the aromatic rings of p-nitrophenyl acetate, phenyl acetate, and nj-nitrophenyl acetate, respectively, are at the heights of 2.2, 1.9 and 1.7 A with respect to the plane comprised of the 6 H-3 atoms of a-cyclodextrin. As shown in Table 1, the calculated values of the anisotropic shielding effects of the aromatic rings of the phenyl acetates on both the H-3 and H-5 atoms agree fairly well with the observed values. 

Fig. 3. Time-averaged conformations of the inclusion complexes of -cyclodextrin with p-nitrophenyl acetate (A), phenyl acetate (B), and m-nitrophenyl acetate (C) in a 1 1 (v/v) mixture of 1 N deuterium...

Fig. 5. The time-averaged conformation of the a-cyclodextrin-m-nitrophenol complex ----------H3— and...

For example, the time-averaged conformation of the inclusion complex between a-cyclodextrin and w-nitrophenol was determined by this method as shown in Fig. 

Table 5 shows the distances between the carbonyl carbon atoms, the electrophilic centers, and the ring comprised of the 6 0-2 atoms of a-cyclodextrin, the nucleophilic centers, estimated from the time-averaged conformations in Fig. 3, as well as the magnitude of the acceleration by a-cyclodextrin. Both values are determined in a 1 1 mixture of water and dimethylsulfoxide. 

Figure 2. Time-averaged conformation of the binary and ternary inclusion complexes.

Intercalation of EtBr into DNA freezes the internal motion of proton and phosphorus localized to a 2-bp-long DNA region, and eventually alters the time-averaged conformation of DNA to a more rigid structure (37). 

When a macromolecular chain is considered as the constituent element of a network, there is some reason to doubt the coincidence of the junction point vector and the axis of time averaged conformations. The deformation of the network by any deviatoric stress field always results in a net reorientation of elements toward the principal axes and the environment of an element must reflect, on the average, this orientation gradient perpendicular to the junction point vector. Those elements that are oriented along the principal axes of deformation are exceptions to this effect because of the absence of reorientation as discussed in the previous section. 

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